Aziz’s R code Bioinformatics
Nur Aziz
2022 5 29
Profiling Gene Expression from GSE and TCGA
Before begin, it’s recommended to read these publications:
- Analysis workflow of publicly available RNA-sequencing datasets
- TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
- TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
- New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
- Unifying cancer and normal RNA sequencing data from different sources
We will make similar results like these :
This is my results for FAM86A :
Normal vs Tumor from Gene Expression Omnibus
Install and load libraries:
Sys.setenv(LANG='en') #change warning to English
Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 10) #prevent connection lost when roaming big chunk
library(GEOquery)
library(limma)
library(tidyverse)
library(dplyr)
library("ggsci")
library(rstatix)To make graph look nice and consistents, I make my own function : 
####Aziz' function's theme and color palettes
scale_fill_aziz <- function(...){
library(scales)
discrete_scale("fill","aziz",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
}
scale_colour_aziz <- function(...){
library(scales)
discrete_scale("colour","aziz",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
}
theme_Publication <- function(base_size=14, base_family="helvetica") {
library(grid)
library(ggthemes)
(theme_foundation(base_size=base_size, base_family=base_family)
+ theme(plot.title = element_text(face = "bold",
size = rel(1.2), hjust = 0.5),
text = element_text(),
panel.background = element_rect(colour = NA),
plot.background = element_rect(colour = NA),
panel.border = element_rect(colour = NA),
axis.title = element_text(face = "bold",size = rel(1)),
axis.title.y = element_text(angle=90,vjust =2),
axis.title.x = element_text(vjust = -0.2),
axis.text = element_text(),
axis.line = element_line(colour="black"),
axis.ticks = element_line(),
panel.grid.major = element_line(colour="#f0f0f0"),
panel.grid.minor = element_blank(),
legend.key = element_rect(colour = NA),
legend.position = "bottom",
legend.direction = "horizontal",
legend.key.size= unit(0.2, "cm"),
legend.margin = unit(0, "cm"),
legend.title = element_text(face="italic"),
plot.margin=unit(c(10,5,5,5),"mm"),
strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"),
strip.text = element_text(face="bold")
))
}#### GSE62254 (ACRG)
gset <- getGEO("GSE66229", GSEMatrix =TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
# make proper column names to match toptable
fvarLabels(gset) <- make.names(fvarLabels(gset))
# group membership for all samples
gsms <- paste0("11100000000000000111110000000000000000100111111111",
"11111111111111111111111111111111111111111111111111",
"11111111111111111111111111111111111111111111111111",
"11111111111111111111111010111101111000000111111111",
"11111111111111111111111111111111111111111111111111",
"11111111111111111111111111111111111111111111111111",
"11111111111111111111111111111111111100000111110000",
"00000000000000000000000000000000000000000000000000")
sml <- strsplit(gsms, split="")[[1]]
# log2 transformation
ex <- exprs(gset)
qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
LogC <- (qx[5] > 100) ||
(qx[6]-qx[1] > 50 && qx[2] > 0)
if (LogC) { ex[which(ex <= 0)] <- NaN
exprs(gset) <- log2(ex) }
# assign samples to groups and set up design matrix
gs <- factor(sml)
groups <- make.names(c("N","T"))
levels(gs) <- groups
gset$group <- gs
design <- model.matrix(~group + 0, gset)
colnames(design) <- levels(gs)
fit <- lmFit(gset, design) # fit linear model
# set up contrasts of interest and recalculate model coefficients
cts <- paste(groups[1], groups[2], sep="-")
cont.matrix <- makeContrasts(contrasts=cts, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
# compute statistics and table of top significant genes
fit2 <- eBayes(fit2, 0.01)
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=250)
tT <- subset(tT, select=c("ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title"))
# Visualize and quality control test results.
# Build histogram of P-values for all genes. Normal test
# assumption is that most genes are not differentially expressed.
tT2 <- topTable(fit2, adjust="fdr", sort.by="B", number=Inf)
hist(tT2$adj.P.Val, col = "grey", border = "white", xlab = "P-adj",
ylab = "Number of genes", main = "P-adj value distribution")
#prepare for only genes passing the threshold
newtT2<-tT2 %>%
filter(adj.P.Val<0.05)
newtT3 <- subset(newtT2,select=c("ID","adj.P.Val","t","B","logFC","Gene.symbol","Gene.title"))
write.csv(newtT3,file="normal tumor acrg fdr ok genes.csv") #you can check the directory
#retrieve the expression of your gene in all patient
threegenes<-ex[row.names(ex) %in% c("219617_at", #camkmt
"222013_x_at", #FAM86A
"206445_s_at"),] #PRMT1
write.csv(threegenes,file="acrg cmt fam prmt1.csv")
# download phenotypes
my.gse <- "GSE66229"
if(!file.exists("geo_downloads")) dir.create("geo_downloads")
if(!file.exists("results")) dir.create("results", recursive=TRUE)
my.geo.gse <- getGEO(GEO=my.gse, filename=NULL, destdir="./geo_downloads", GSElimits=NULL, GSEMatrix=TRUE, AnnotGPL=FALSE, getGPL=FALSE)
my.geo.gse <- my.geo.gse[[1]]
my.pdata <- as.data.frame(pData(my.geo.gse), stringsAsFactors=F)
write.csv(my.pdata,file="phenotype acrg.csv")#assign Expression data with phenotype in excel (efficient using vlookup formula) : format like below
nt<-read.csv('graph nt acrg.csv',sep='\t')
head(nt)## ID PRMT1 CAMKMT FAM86A Tissue
## 1 GSM1523727 2.957375 1.999631 1.758549 T
## 2 GSM1523728 3.128566 1.689934 1.830104 T
## 3 GSM1523729 3.052887 1.806846 1.791574 T
## 4 GSM1523730 2.916911 1.659223 1.750806 N
## 5 GSM1523731 2.789613 1.710085 1.744396 N
## 6 GSM1523732 3.088736 1.715045 1.766945 Nacrg<-nt
acrg<-acrg %>%
mutate(Tissue2 = case_when(Tissue == 'N' ~ 'Normal',
Tissue == 'T' ~ 'Tumor'))
acrg$Tissue2 <- factor(acrg$Tissue2, levels = c("Normal", "Tumor"))
GSEacrg<-ggplot(acrg,aes(x=Tissue2,y=FAM86A,fill=Tissue2))+
labs(y=expression('FAM86A expression (log'[10]*")"),x=NULL)+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text.x = element_text(),
legend.position = 'none',
axis.title.x = element_blank(),
panel.grid.major.x = element_blank(),
aspect.ratio = 1.85)
GSEacrg
#statistical analysis
wilcox.test(FAM86A ~ Tissue2, data = acrg,
exact = FALSE)##
## Wilcoxon rank sum test with continuity correction
##
## data: FAM86A by Tissue2
## W = 11848, p-value = 0.001646
## alternative hypothesis: true location shift is not equal to 0acrg %>% wilcox_effsize(FAM86A ~ Tissue2)## # A tibble: 1 x 7
## .y. group1 group2 effsize n1 n2 magnitude
## * <chr> <chr> <chr> <dbl> <int> <int> <ord>
## 1 FAM86A Normal Tumor 0.157 100 300 smallgset <- getGEO("GSE54129", GSEMatrix =TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
# make proper column names to match toptable
fvarLabels(gset) <- make.names(fvarLabels(gset))
# group membership for all samples
gsms <- paste0("00000000000000000000011111111111111111111111111111",
"11111111111111111111111111111111111111111111111111",
"11111111111111111111111111111111")
sml <- strsplit(gsms, split="")[[1]]
# log2 transformation
ex <- exprs(gset)
qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
LogC <- (qx[5] > 100) ||
(qx[6]-qx[1] > 50 && qx[2] > 0)
if (LogC) { ex[which(ex <= 0)] <- NaN
exprs(gset) <- log2(ex) }
# assign samples to groups and set up design matrix
gs <- factor(sml)
groups <- make.names(c("N","T"))
levels(gs) <- groups
gset$group <- gs
design <- model.matrix(~group + 0, gset)
colnames(design) <- levels(gs)
fit <- lmFit(gset, design) # fit linear model
# set up contrasts of interest and recalculate model coefficients
cts <- paste(groups[1], groups[2], sep="-")
cont.matrix <- makeContrasts(contrasts=cts, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
# compute statistics and table of top significant genes
fit2 <- eBayes(fit2, 0.01)
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=250)
tT <- subset(tT, select=c("ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title"))
# Visualize and quality control test results.
# Build histogram of P-values for all genes. Normal test
# assumption is that most genes are not differentially expressed.
tT2 <- topTable(fit2, adjust="fdr", sort.by="B", number=Inf)
hist(tT2$adj.P.Val, col = "grey", border = "white", xlab = "P-adj",
ylab = "Number of genes", main = "P-adj value distribution")
# summarize test results as "up", "down" or "not expressed"
dT <- decideTests(fit2, adjust.method="fdr", p.value=0.05)
# Venn diagram of results
vennDiagram(dT, circle.col=palette())
#our code start
newtT2<-tT2 %>%
filter(adj.P.Val<0.05)
newtT3 <- subset(newtT2,select=c("ID","adj.P.Val","t","B","logFC","Gene.symbol","Gene.title"))
write.csv(newtT3,file="normal tumor GSE54129 fdr ok genes.csv")
####################expression of selected genes############
threegenes<-ex[row.names(ex) %in% c("219617_at", #camkmt
"222013_x_at", #FAM86A
"206445_s_at"),]#PRMT1
write.csv(threegenes,file="GSE54129 cmt fam prmt1.csv")
#####################phenotypes
my.gse <- "GSE54129"
if(!file.exists("geo_downloads")) dir.create("geo_downloads")
if(!file.exists("results")) dir.create("results", recursive=TRUE)
my.geo.gse <- getGEO(GEO=my.gse, filename=NULL, destdir="./geo_downloads", GSElimits=NULL, GSEMatrix=TRUE, AnnotGPL=FALSE, getGPL=FALSE)
my.geo.gse <- my.geo.gse[[1]]
my.pdata <- as.data.frame(pData(my.geo.gse), stringsAsFactors=F)
write.csv(my.pdata,file="phenotype GSE54129.csv")
#plot
G129<-read.csv('graph nt GSE54129.csv',sep='\t')
head(G129)## ID PRMT1 CAMKMT FAM86A Tissue
## 1 GSM1308392 9.452179 6.115939 6.425237 N
## 2 GSM1308393 9.443866 5.661901 6.131955 N
## 3 GSM1308394 8.921622 5.910835 6.128566 N
## 4 GSM1308395 8.664146 5.537663 6.460649 N
## 5 GSM1308396 8.938331 5.695038 6.163880 N
## 6 GSM1308397 9.011761 5.955174 6.169497 NG129<-G129 %>%
mutate(Tissue2 = case_when(Tissue == 'N' ~ 'Normal',
Tissue == 'T' ~ 'Tumor'))
G129$Tissue2 <- factor(G129$Tissue2, levels = c("Normal", "Tumor"))
GSE4129<-ggplot(G129,aes(x=Tissue2,y=FAM86A,fill=Tissue2))+
labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text.x = element_text(),
legend.position = 'none',
axis.title.x = element_blank(),
panel.grid.major.x = element_blank(),
aspect.ratio = 1.85)
GSE4129
#statistical analysis
wilcox.test(FAM86A ~ Tissue2, data = G129,
exact = FALSE)##
## Wilcoxon rank sum test with continuity correction
##
## data: FAM86A by Tissue2
## W = 475, p-value = 1.764e-05
## alternative hypothesis: true location shift is not equal to 0G129 %>% wilcox_effsize(FAM86A ~ Tissue2)## # A tibble: 1 x 7
## .y. group1 group2 effsize n1 n2 magnitude
## * <chr> <chr> <chr> <dbl> <int> <int> <ord>
## 1 FAM86A Normal Tumor 0.374 21 111 moderateUnify GTEx NAT and Tumor TCGA
- datasets retrieve from [nature scientific data] (doi.org/10.1038/sdata.2018.61)
- fisrt load the all 3 datasets (tcga normal, tcga tumor, and gtex -> FPKM normalized Combat batch correction)
stomach.rsem.fpkm.gtex <- read.delim("~/stomach-rsem-fpkm-gtex.txt")
stad.rsem.fpkm.tcga.t <- read.delim("~/stad-rsem-fpkm-tcga-t.txt")
stad.rsem.fpkm.tcga <- read.delim("~/stad-rsem-fpkm-tcga.txt")
df.gtex<-stomach.rsem.fpkm.gtex
df.t.tcga<-stad.rsem.fpkm.tcga.t
df.n.tcga<-stad.rsem.fpkm.tcga
library(tidyverse)
library(dplyr)
Sys.setenv(LANG='en')
############GTEx###############
colnames(df.gtex)## [1] "Hugo_Symbol" "Entrez_Gene_Id"
## [3] "GTEX.QCQG.0526.SM.48U2A" "GTEX.QDVJ.1426.SM.48U1Y"
## [5] "GTEX.13111.1226.SM.5GCNC" "GTEX.S4Z8.1226.SM.4AD6W"
## [7] "GTEX.ZDYS.1926.SM.5HL59" "GTEX.144GM.1726.SM.5O9AS"
## [9] "GTEX.PWOO.1226.SM.48TCO" "GTEX.146FR.2026.SM.5NQAI"
## [11] "GTEX.1399R.1126.SM.5IFIO" "GTEX.WHWD.1426.SM.4OORU"
## [13] "GTEX.111CU.0926.SM.5EGIK" "GTEX.WZTO.2126.SM.4PQYW"
## [15] "GTEX.T8EM.1226.SM.4DM5J" "GTEX.NFK9.1526.SM.3LK7B"
## [17] "GTEX.YEC4.1426.SM.5IFHS" "GTEX.T5JC.1926.SM.4DM6Q"
## [19] "GTEX.WFG8.1326.SM.4LVN3" "GTEX.OXRK.1626.SM.3NB17"
## [21] "GTEX.P4PQ.1526.SM.3NMCK" "GTEX.ZA64.0826.SM.5HL9U"
## [23] "GTEX.1399S.1626.SM.5P9GI" "GTEX.R55C.1026.SM.48FCM"
## [25] "GTEX.P4PP.1526.SM.3P61M" "GTEX.13OVI.2426.SM.5KM4J"
## [27] "GTEX.146FH.2126.SM.5SI9U" "GTEX.145ME.1026.SM.5O9B4"
## [29] "GTEX.13113.0726.SM.5LZUF" "GTEX.13X6H.1626.SM.5Q5CT"
## [31] "GTEX.13O3Q.2126.SM.5KM4C" "GTEX.WHPG.0426.SM.4M1XW"
## [33] "GTEX.Y8E4.1526.SM.4WWDI" "GTEX.ZE7O.3026.SM.51MS4"
## [35] "GTEX.VJYA.1026.SM.4KL21" "GTEX.S4Q7.0726.SM.4AD5F"
## [37] "GTEX.U8T8.1226.SM.4E3IH" "GTEX.Y114.1226.SM.4TT88"
## [39] "GTEX.1211K.1426.SM.5FQTF" "GTEX.RM2N.0826.SM.48FD3"
## [41] "GTEX.12696.1726.SM.5EQLH" "GTEX.12WSG.2026.SM.5FQUU"
## [43] "GTEX.OOBJ.1526.SM.3NB1Q" "GTEX.PX3G.1526.SM.48U11"
## [45] "GTEX.WFON.1126.SM.4LVMA" "GTEX.11P82.0726.SM.5PNYL"
## [47] "GTEX.QV31.0626.SM.447C5" "GTEX.R55G.1126.SM.48FDG"
## [49] "GTEX.14BMU.1126.SM.5RQJ8" "GTEX.SIU7.1426.SM.4BRWT"
## [51] "GTEX.Q2AH.1126.SM.48TZM" "GTEX.13OW6.2526.SM.5IJEC"
## [53] "GTEX.13O61.1126.SM.5L3FI" "GTEX.XBEW.1826.SM.4RTWX"
## [55] "GTEX.S341.0626.SM.4AD5T" "GTEX.ZT9W.1526.SM.4YCDE"
## [57] "GTEX.13QJ3.2726.SM.5SI6L" "GTEX.RU1J.0526.SM.46MUT"
## [59] "GTEX.XAJ8.0326.SM.47JYI" "GTEX.PW2O.1226.SM.48TCH"
## [61] "GTEX.12WSK.1426.SM.5CVNN" "GTEX.SNOS.0826.SM.4DM5N"
## [63] "GTEX.YEC3.1426.101806.SM.5PNXX" "GTEX.11VI4.0326.SM.5EQ6L"
## [65] "GTEX.132AR.2426.SM.5IFFD" "GTEX.W5WG.1726.SM.4LMI5"
## [67] "GTEX.Y5LM.1326.SM.5RQIS" "GTEX.PWCY.0926.SM.48TD7"
## [69] "GTEX.ZVT2.1626.SM.51MRC" "GTEX.S3XE.1026.SM.4AD4O"
## [71] "GTEX.13D11.2126.SM.5IFH2" "GTEX.XUZC.0726.SM.4BOPH"
## [73] "GTEX.QMRM.1126.SM.447BN" "GTEX.XBED.1226.SM.4AT5V"
## [75] "GTEX.X15G.1126.SM.4PQZG" "GTEX.Q734.1026.SM.48U16"
## [77] "GTEX.1399U.1626.SM.5P9J3" "GTEX.RWS6.0926.SM.47JXE"
## [79] "GTEX.TKQ2.0926.SM.4DXU5" "GTEX.12C56.0526.SM.5FQST"
## [81] "GTEX.145LT.1426.SM.5O9B3" "GTEX.S4P3.0726.SM.4AD57"
## [83] "GTEX.13FTX.0726.SM.5N9BI" "GTEX.ZLV1.0826.SM.4WWEQ"
## [85] "GTEX.11NUK.2426.SM.5BC4U" "GTEX.ZVP2.1626.SM.5GU5D"
## [87] "GTEX.ZF2S.1426.SM.57WET" "GTEX.12WSD.2326.SM.59HKQ"
## [89] "GTEX.U3ZN.2026.SM.4DXUC" "GTEX.133LE.1326.SM.5IFGO"
## [91] "GTEX.1122O.1926.SM.5EGIQ" "GTEX.11TT1.0726.SM.5GU5A"
## [93] "GTEX.R53T.1226.SM.48FCT" "GTEX.ZAB4.1526.SM.5CVN7"
## [95] "GTEX.11EQ9.1226.SM.5987E" "GTEX.144GN.1226.SM.5O991"
## [97] "GTEX.145MN.1326.SM.5NQ9S" "GTEX.1339X.1426.SM.5K7YO"
## [99] "GTEX.Y9LG.1026.SM.5IFJN" "GTEX.ZQUD.0826.SM.57WDQ"
## [101] "GTEX.13U4I.2526.SM.5SI8Z" "GTEX.OHPK.1526.SM.3MJGM"
## [103] "GTEX.P4QT.1526.SM.3NMCT" "GTEX.QLQ7.0826.SM.447B3"
## [105] "GTEX.ZXES.1426.SM.5NQ8S" "GTEX.RTLS.2626.SM.46MUJ"
## [107] "GTEX.QV44.1226.SM.4R1KE" "GTEX.YJ8A.1526.SM.5P9FT"
## [109] "GTEX.13PVQ.2126.SM.5L3FW" "GTEX.TMMY.1626.SM.4DXTY"
## [111] "GTEX.ZTX8.0426.SM.59HLG" "GTEX.14BMV.2226.SM.5RQHX"
## [113] "GTEX.XV7Q.1326.SM.4BRWM" "GTEX.145MO.2226.SM.5Q5BN"
## [115] "GTEX.QXCU.1926.SM.48FE4" "GTEX.117YW.2226.SM.5N9DB"
## [117] "GTEX.13FTW.1726.SM.5KM2B" "GTEX.ZV6S.0926.SM.57WGB"
## [119] "GTEX.WH7G.1526.SM.4LVMX" "GTEX.XQ8I.2026.SM.4BOOL"
## [121] "GTEX.YFCO.0826.SM.5LUAG" "GTEX.SNMC.0626.SM.4DM6H"
## [123] "GTEX.UPIC.1826.SM.4IHKC" "GTEX.ZVZP.1726.SM.5GZWY"
## [125] "GTEX.ZZPU.1426.SM.5GZZ6" "GTEX.139D8.2326.SM.5IFGE"
## [127] "GTEX.139YR.1926.SM.5LZXM" "GTEX.T6MO.0726.SM.4DM58"
## [129] "GTEX.11I78.1726.SM.5A5M3" "GTEX.T5JW.0926.SM.4DM5K"
## [131] "GTEX.Y5V6.1326.SM.4VDTF" "GTEX.111YS.1126.SM.5GZYQ"
## [133] "GTEX.S95S.0826.SM.4B64N" "GTEX.13S7M.1826.SM.5RQK6"
## [135] "GTEX.UJHI.1026.SM.4IHJP" "GTEX.11GSP.2126.SM.5HL5E"
## [137] "GTEX.13O21.0926.SM.5IFGT" "GTEX.12BJ1.1726.SM.5HL9B"
## [139] "GTEX.117YX.1026.SM.5H11V" "GTEX.11NSD.1426.SM.5HL67"
## [141] "GTEX.12WSJ.0926.SM.5P9JD" "GTEX.13QBU.1126.SM.5LU44"
## [143] "GTEX.ZY6K.0726.SM.5A5L8" "GTEX.V955.1326.SM.4JBHR"
## [145] "GTEX.ZYVF.2726.SM.5GID4" "GTEX.POMQ.0826.SM.3P61H"
## [147] "GTEX.WFG7.1326.SM.4LMK1" "GTEX.QLQW.0726.SM.447AA"
## [149] "GTEX.XUJ4.1226.SM.4BOPD" "GTEX.11DXX.1326.SM.5GIDZ"
## [151] "GTEX.ZPIC.2026.SM.57WG3" "GTEX.Y3IK.1426.SM.4YCES"
## [153] "GTEX.ZYY3.1726.SM.5EGH3" "GTEX.PLZ6.0826.SM.3P61K"
## [155] "GTEX.QDVN.1226.SM.48TZ5" "GTEX.OIZH.1526.SM.3NB1J"
## [157] "GTEX.13N1W.2026.SM.5K7YU" "GTEX.131XF.1226.SM.5HL8V"
## [159] "GTEX.13CF3.1926.SM.5K7WF" "GTEX.11EM3.1026.SM.5A5KL"
## [161] "GTEX.13FH7.1026.SM.5IJGF" "GTEX.UPK5.2126.SM.4JBJK"
## [163] "GTEX.Y8LW.0826.SM.4WWDO" "GTEX.ZZ64.0426.SM.5E43F"
## [165] "GTEX.ZLFU.1326.SM.4WWET" "GTEX.UJMC.1226.SM.4IHLI"
## [167] "GTEX.131XE.2226.SM.5PNYX" "GTEX.R55D.1526.SM.48FEJ"
## [169] "GTEX.S4UY.1626.SM.4AD55" "GTEX.O5YW.1526.SM.3MJGL"
## [171] "GTEX.V1D1.1726.SM.4JBHB" "GTEX.ZYFG.1326.SM.5GICJ"
## [173] "GTEX.ZVT3.2126.SM.59HL2" "GTEX.XXEK.0826.SM.4BRWG"
## [175] "GTEX.Y3I4.1626.SM.4TT7W" "GTEX.WEY5.1226.SM.4LMIQ"
## [177] "GTEX.PWN1.1526.SM.48TDA" "GTEX.Q2AI.0826.SM.48TZO"
## [179] "GTEX.TKQ1.0526.SM.4DXTG" "GTEX.11WQK.2626.SM.5EQ4K"
## [181] "GTEX.WFJO.1126.SM.4LVLZ" "GTEX.11P7K.1726.SM.5GU6F"
## [183] "GTEX.U4B1.1026.SM.4DXT1" "GTEX.WRHK.0626.SM.4MVOE"
## [185] "GTEX.13RTK.0226.SM.5RQHR" "GTEX.11EI6.2426.SM.5PNVS"
## [187] "GTEX.P78B.1826.SM.3P5YX" "GTEX.S7SF.0626.SM.4AD4V"
## [189] "GTEX.XPVG.1526.SM.4B66C" "GTEX.132QS.1826.SM.5IFFN"
## [191] "GTEX.ZPU1.1626.SM.4WWB2" "GTEX.ZP4G.1226.SM.4WWCJ"
## [193] "GTEX.131XG.1226.SM.5EGH9" "GTEX.ZV7C.1626.SM.5NQ7E"df.gtex.FAM86A<-df.gtex %>%
filter(Hugo_Symbol == 'FAM86A')
head(df.gtex.FAM86A)[2]## Entrez_Gene_Id
## 1 196483dim(df.gtex.FAM86A)## [1] 1 194#transposing
df.gtex.FAM86A<-df.gtex.FAM86A %>%
gather(Patients,FPKM,3:ncol(.))
dim(df.gtex.FAM86A)## [1] 192 4head(df.gtex.FAM86A)## Hugo_Symbol Entrez_Gene_Id Patients FPKM
## 1 FAM86A 196483 GTEX.QCQG.0526.SM.48U2A 224.97
## 2 FAM86A 196483 GTEX.QDVJ.1426.SM.48U1Y 220.32
## 3 FAM86A 196483 GTEX.13111.1226.SM.5GCNC 121.79
## 4 FAM86A 196483 GTEX.S4Z8.1226.SM.4AD6W 185.11
## 5 FAM86A 196483 GTEX.ZDYS.1926.SM.5HL59 171.45
## 6 FAM86A 196483 GTEX.144GM.1726.SM.5O9AS 185.11df.gtex.FAM86A.log2<-df.gtex.FAM86A %>%
mutate(log2FPKM=log(FPKM,base = 2))
head(df.gtex.FAM86A.log2)## Hugo_Symbol Entrez_Gene_Id Patients FPKM log2FPKM
## 1 FAM86A 196483 GTEX.QCQG.0526.SM.48U2A 224.97 7.813589
## 2 FAM86A 196483 GTEX.QDVJ.1426.SM.48U1Y 220.32 7.783457
## 3 FAM86A 196483 GTEX.13111.1226.SM.5GCNC 121.79 6.928252
## 4 FAM86A 196483 GTEX.S4Z8.1226.SM.4AD6W 185.11 7.532239
## 5 FAM86A 196483 GTEX.ZDYS.1926.SM.5HL59 171.45 7.421644
## 6 FAM86A 196483 GTEX.144GM.1726.SM.5O9AS 185.11 7.532239#######NAT###########
colnames(df.n.tcga)## [1] "Hugo_Symbol" "Entrez_Gene_Id"
## [3] "TCGA.BR.6564.11A.01R.1884.13" "TCGA.HU.A4GH.11A.11R.A36D.31"
## [5] "TCGA.IN.8663.11A.01R.2402.13" "TCGA.HU.8238.11A.01R.2343.13"
## [7] "TCGA.BR.7716.11A.01R.2055.13" "TCGA.FP.7735.11A.01R.2055.13"
## [9] "TCGA.HU.A4GY.11A.11R.A36D.31" "TCGA.IN.AB1X.11A.21R.A39E.31"
## [11] "TCGA.CG.5720.11A.01R.1602.13" "TCGA.IN.8462.11A.01R.2343.13"
## [13] "TCGA.BR.7704.11A.01R.2055.13" "TCGA.CG.5722.11A.02R.1602.13"
## [15] "TCGA.BR.6458.11A.01R.1802.13" "TCGA.HU.A4HB.11A.11R.A251.31"
## [17] "TCGA.CG.5734.11A.01R.1602.13" "TCGA.IN.AB1V.11A.11R.A414.31"
## [19] "TCGA.FP.7829.11A.01R.2055.13" "TCGA.BR.6453.11A.01R.1802.13"
## [21] "TCGA.BR.6457.11A.01R.1802.13" "TCGA.IP.7968.11A.01R.2203.13"
## [23] "TCGA.HU.A4GN.11A.12R.A251.31" "TCGA.HU.A4GP.11A.21R.A251.31"
## [25] "TCGA.CG.5730.11A.01R.1602.13" "TCGA.IN.7806.11A.01R.2055.13"
## [27] "TCGA.BR.6454.11A.01R.1802.13" "TCGA.BR.7715.11A.01R.2055.13"
## [29] "TCGA.CG.5733.11A.01R.1602.13" "TCGA.BR.6852.11A.01R.1884.13"
## [31] "TCGA.BR.6802.11A.01R.1884.13" "TCGA.HU.A4G3.11A.11R.A24K.31"
## [33] "TCGA.BR.7851.11A.01R.2203.13" "TCGA.CG.5721.11A.01R.1602.13"
## [35] "TCGA.BR.7717.11A.01R.2055.13"df.n.tcga.FAM86A<-df.n.tcga %>%
filter(Hugo_Symbol == 'FAM86A')
head(df.n.tcga.FAM86A)[2]## Entrez_Gene_Id
## 1 196483dim(df.n.tcga.FAM86A)## [1] 1 35#transposing
df.n.tcga.FAM86A<-df.n.tcga.FAM86A %>%
gather(Patients,FPKM,3:ncol(.))
dim(df.n.tcga.FAM86A)## [1] 33 4head(df.n.tcga.FAM86A)## Hugo_Symbol Entrez_Gene_Id Patients FPKM
## 1 FAM86A 196483 TCGA.BR.6564.11A.01R.1884.13 220.32
## 2 FAM86A 196483 TCGA.HU.A4GH.11A.11R.A36D.31 202.66
## 3 FAM86A 196483 TCGA.IN.8663.11A.01R.2402.13 166.73
## 4 FAM86A 196483 TCGA.HU.8238.11A.01R.2343.13 163.28
## 5 FAM86A 196483 TCGA.BR.7716.11A.01R.2055.13 249.73
## 6 FAM86A 196483 TCGA.FP.7735.11A.01R.2055.13 256.78df.n.tcga.FAM86A.log2<-df.n.tcga.FAM86A %>%
mutate(log2FPKM=log(FPKM,base = 2))
head(df.n.tcga.FAM86A.log2)## Hugo_Symbol Entrez_Gene_Id Patients FPKM log2FPKM
## 1 FAM86A 196483 TCGA.BR.6564.11A.01R.1884.13 220.32 7.783457
## 2 FAM86A 196483 TCGA.HU.A4GH.11A.11R.A36D.31 202.66 7.662918
## 3 FAM86A 196483 TCGA.IN.8663.11A.01R.2402.13 166.73 7.381370
## 4 FAM86A 196483 TCGA.HU.8238.11A.01R.2343.13 163.28 7.351204
## 5 FAM86A 196483 TCGA.BR.7716.11A.01R.2055.13 249.73 7.964225
## 6 FAM86A 196483 TCGA.FP.7735.11A.01R.2055.13 256.78 8.004389#######Tumor###########
colnames(df.t.tcga)## [1] "Hugo_Symbol" "Entrez_Gene_Id"
## [3] "TCGA.BR.6457.01A.21R.1802.13" "TCGA.VQ.A8PD.01A.11R.A414.31"
## [5] "TCGA.BR.6803.01A.11R.1884.13" "TCGA.VQ.A8E3.01A.11R.A39E.31"
## [7] "TCGA.CG.5718.01A.11R.1602.13" "TCGA.VQ.A8E2.01A.11R.A36D.31"
## [9] "TCGA.CD.5799.01A.11R.1602.13" "TCGA.BR.6452.01A.12R.1802.13"
## [11] "TCGA.CG.4438.01A.01R.1157.13" "TCGA.BR.4257.01A.01R.1131.13"
## [13] "TCGA.CD.A48C.01A.11R.A24K.31" "TCGA.D7.5577.01A.01R.1602.13"
## [15] "TCGA.BR.A4IV.01A.31R.A251.31" "TCGA.FP.8631.01A.11R.2402.13"
## [17] "TCGA.BR.A452.01A.91R.A251.31" "TCGA.BR.4187.01A.01R.1131.13"
## [19] "TCGA.BR.6706.01A.11R.1884.13" "TCGA.CD.5803.01A.11R.1602.13"
## [21] "TCGA.VQ.AA6B.01A.11R.A414.31" "TCGA.BR.8295.01A.11R.2343.13"
## [23] "TCGA.BR.8059.01A.11R.2343.13" "TCGA.CG.5724.01A.11R.1602.13"
## [25] "TCGA.F1.6177.01A.11R.1802.13" "TCGA.HU.A4GH.01A.11R.A24K.31"
## [27] "TCGA.HU.8608.01A.11R.2402.13" "TCGA.BR.6456.01A.11R.1802.13"
## [29] "TCGA.BR.A4IZ.01A.32R.A251.31" "TCGA.BR.A4PF.01A.11R.A251.31"
## [31] "TCGA.RD.A8N5.01A.12R.A36D.31" "TCGA.HU.8610.01A.22R.2402.13"
## [33] "TCGA.HU.A4GQ.01A.11R.A36D.31" "TCGA.HU.A4HD.01A.11R.A251.31"
## [35] "TCGA.HU.A4HB.01A.12R.A251.31" "TCGA.VQ.A925.01A.11R.A414.31"
## [37] "TCGA.BR.6852.01A.11R.1884.13" "TCGA.BR.4292.01A.01R.1131.13"
## [39] "TCGA.BR.6705.01A.12R.1884.13" "TCGA.BR.A4J5.01A.21R.A251.31"
## [41] "TCGA.BR.6709.01A.11R.1884.13" "TCGA.MX.A666.01A.11R.A31P.31"
## [43] "TCGA.BR.A4QI.01A.12R.A251.31" "TCGA.BR.7959.01A.11R.2343.13"
## [45] "TCGA.D7.8576.01A.11R.2343.13" "TCGA.VQ.A8E0.01A.11R.A414.31"
## [47] "TCGA.VQ.A91A.01A.11R.A414.31" "TCGA.F1.A72C.01A.21R.A33Y.31"
## [49] "TCGA.D7.8578.01A.21R.2343.13" "TCGA.CG.5732.01A.11R.1602.13"
## [51] "TCGA.BR.6707.01A.11R.1884.13" "TCGA.VQ.AA6I.01A.11R.A414.31"
## [53] "TCGA.BR.8060.01A.11R.2343.13" "TCGA.F1.A448.01A.11R.A24K.31"
## [55] "TCGA.VQ.A8E7.01B.11R.A414.31" "TCGA.RD.A8N9.01A.12R.A39E.31"
## [57] "TCGA.HU.A4GF.01A.11R.A24K.31" "TCGA.BR.4367.01A.01R.1157.13"
## [59] "TCGA.VQ.A923.01A.11R.A414.31" "TCGA.CG.5720.01A.11R.1602.13"
## [61] "TCGA.HU.8602.01A.11R.2402.13" "TCGA.CG.4477.01A.01R.1157.13"
## [63] "TCGA.D7.6822.01A.11R.1884.13" "TCGA.CD.8526.01A.11R.2343.13"
## [65] "TCGA.D7.A6EY.01A.21R.A31P.31" "TCGA.CD.5798.01A.11R.1602.13"
## [67] "TCGA.R5.A805.01A.11R.A36D.31" "TCGA.BR.6455.01A.11R.1802.13"
## [69] "TCGA.HU.A4GJ.01A.11R.A251.31" "TCGA.BR.8297.01A.12R.2343.13"
## [71] "TCGA.BR.8372.01A.11R.2343.13" "TCGA.HU.A4GY.01A.21R.A24K.31"
## [73] "TCGA.VQ.A94P.01A.13R.A414.31" "TCGA.BR.8590.01A.11R.2402.13"
## [75] "TCGA.BR.7703.01A.11R.2055.13" "TCGA.VQ.A91Y.01A.11R.A414.31"
## [77] "TCGA.HU.A4H6.01A.11R.A251.31" "TCGA.VQ.A8PC.01A.11R.A39E.31"
## [79] "TCGA.R5.A7ZF.01A.11R.A354.31" "TCGA.HU.A4GN.01A.11R.A251.31"
## [81] "TCGA.BR.8286.01A.12R.2343.13" "TCGA.D7.6818.01A.11R.1884.13"
## [83] "TCGA.CG.4442.01A.01R.1157.13" "TCGA.VQ.A91S.01A.11R.A414.31"
## [85] "TCGA.MX.A5UG.01A.21R.A31P.31" "TCGA.D7.A748.01A.12R.A32D.31"
## [87] "TCGA.VQ.AA6K.01A.11R.A414.31" "TCGA.BR.8371.01A.11R.2343.13"
## [89] "TCGA.VQ.AA6D.01A.11R.A414.31" "TCGA.CG.4469.01A.01R.1157.13"
## [91] "TCGA.CG.4472.01A.01R.1157.13" "TCGA.MX.A5UJ.01A.11R.A31P.31"
## [93] "TCGA.VQ.A91U.01A.11R.A414.31" "TCGA.VQ.A91E.01A.31R.A414.31"
## [95] "TCGA.HU.A4GP.01A.11R.A251.31" "TCGA.BR.8682.01A.11R.2402.13"
## [97] "TCGA.BR.8361.01A.11R.2343.13" "TCGA.VQ.AA6A.01A.11R.A414.31"
## [99] "TCGA.R5.A7O7.01A.11R.A33Y.31" "TCGA.CG.4444.01A.01R.1157.13"
## [101] "TCGA.BR.A4J4.01A.12R.A251.31" "TCGA.BR.8485.01A.11R.2402.13"
## [103] "TCGA.BR.A4CR.01A.11R.A24K.31" "TCGA.BR.8487.01A.11R.2402.13"
## [105] "TCGA.D7.A4Z0.01A.22R.A251.31" "TCGA.FP.8099.01A.11R.2343.13"
## [107] "TCGA.BR.A44T.01A.32R.A24K.31" "TCGA.BR.8680.01A.11R.2402.13"
## [109] "TCGA.HU.8243.01A.11R.2343.13" "TCGA.D7.A6F2.01A.12R.A31P.31"
## [111] "TCGA.CG.4474.01A.02R.1157.13" "TCGA.VQ.A91X.01A.12R.A414.31"
## [113] "TCGA.BR.8677.01A.11R.2402.13" "TCGA.RD.A8N0.01A.12R.A36D.31"
## [115] "TCGA.IN.AB1X.01A.11R.A39E.31" "TCGA.RD.A8N1.01A.12R.A36D.31"
## [117] "TCGA.EQ.8122.01A.11R.2343.13" "TCGA.B7.A5TI.01A.11R.A31P.31"
## [119] "TCGA.HU.A4H4.01A.21R.A251.31" "TCGA.IN.AB1V.01A.21R.A414.31"
## [121] "TCGA.BR.7722.01A.31R.2203.13" "TCGA.HF.7134.01A.11R.2055.13"
## [123] "TCGA.BR.7715.01A.11R.2055.13" "TCGA.CG.5722.01A.21R.1602.13"
## [125] "TCGA.BR.8369.01A.11R.2343.13" "TCGA.F1.6875.01A.11R.2055.13"
## [127] "TCGA.RD.A8N2.01A.12R.A36D.31" "TCGA.BR.A453.01A.11R.A24K.31"
## [129] "TCGA.BR.6454.01A.11R.1802.13" "TCGA.HU.A4H5.01A.21R.A251.31"
## [131] "TCGA.VQ.A91V.01A.11R.A414.31" "TCGA.BR.A4IU.01A.22R.A251.31"
## [133] "TCGA.BR.7851.01A.11R.2203.13" "TCGA.BR.8367.01A.11R.2343.13"
## [135] "TCGA.HU.A4G9.01A.11R.A24K.31" "TCGA.KB.A6F7.01A.12R.A32D.31"
## [137] "TCGA.CD.A48A.01A.12R.A36D.31" "TCGA.BR.8678.01A.11R.2402.13"
## [139] "TCGA.VQ.A94U.01A.12R.A414.31" "TCGA.VQ.A927.01A.12R.A414.31"
## [141] "TCGA.BR.A4PD.01A.11R.A251.31" "TCGA.BR.7958.01A.21R.2343.13"
## [143] "TCGA.D7.6521.01A.11R.1802.13" "TCGA.VQ.A924.01A.11R.A414.31"
## [145] "TCGA.IN.A6RO.01A.12R.A33Y.31" "TCGA.RD.A7BT.01A.11R.A33Y.31"
## [147] "TCGA.BR.4191.01A.02R.1131.13" "TCGA.D7.A6EZ.01A.11R.A31P.31"
## [149] "TCGA.CG.5723.01A.11R.1602.13" "TCGA.CG.5726.01A.11R.1602.13"
## [151] "TCGA.CG.4440.01A.01R.1157.13" "TCGA.VQ.AA68.01A.11R.A414.31"
## [153] "TCGA.VQ.A92D.01A.11R.A414.31" "TCGA.CG.5734.01A.11R.1602.13"
## [155] "TCGA.BR.A4PE.01A.31R.A251.31" "TCGA.IN.8462.01A.11R.2343.13"
## [157] "TCGA.HU.A4G3.01A.11R.A24K.31" "TCGA.HF.7132.01A.11R.2055.13"
## [159] "TCGA.FP.8210.01A.11R.2343.13" "TCGA.D7.5578.01A.01R.1602.13"
## [161] "TCGA.BR.6564.01A.12R.1884.13" "TCGA.BR.8365.01A.21R.2343.13"
## [163] "TCGA.BR.8078.01A.11R.2343.13" "TCGA.CG.4304.01A.01R.1157.13"
## [165] "TCGA.B7.A5TJ.01A.11R.A31P.31" "TCGA.D7.A6EX.01A.11R.A31P.31"
## [167] "TCGA.D7.8570.01A.11R.2343.13" "TCGA.CD.5800.01A.11R.1602.13"
## [169] "TCGA.HU.A4H3.01A.21R.A251.31" "TCGA.BR.4371.01A.01R.1157.13"
## [171] "TCGA.HF.7131.01A.11R.2055.13" "TCGA.D7.6518.01A.11R.1802.13"
## [173] "TCGA.BR.8368.01A.11R.2343.13" "TCGA.RD.A8NB.01A.12R.A39E.31"
## [175] "TCGA.HU.A4G8.01A.11R.A251.31" "TCGA.IP.7968.01A.11R.2203.13"
## [177] "TCGA.IN.A6RI.01A.11R.A32D.31" "TCGA.VQ.A8P5.01A.11R.A39E.31"
## [179] "TCGA.BR.4201.01A.01R.1131.13" "TCGA.BR.4362.01A.01R.1157.13"
## [181] "TCGA.CG.5725.01A.11R.1602.13" "TCGA.BR.7957.01A.11R.2203.13"
## [183] "TCGA.BR.4280.01A.01R.1131.13" "TCGA.FP.A8CX.01A.11R.A36D.31"
## [185] "TCGA.BR.8591.01A.11R.2402.13" "TCGA.D7.8575.01A.11R.2343.13"
## [187] "TCGA.CD.8534.01A.11R.2343.13" "TCGA.BR.8362.01A.11R.2343.13"
## [189] "TCGA.HF.A5NB.01A.11R.A31P.31" "TCGA.D7.A4YT.01A.11R.A251.31"
## [191] "TCGA.BR.4256.01A.01R.1131.13" "TCGA.BR.4255.01A.01R.1131.13"
## [193] "TCGA.BR.8289.01A.11R.2343.13" "TCGA.BR.8366.01A.11R.2343.13"
## [195] "TCGA.VQ.A94O.01A.11R.A414.31" "TCGA.D7.A4YU.01A.21R.A251.31"
## [197] "TCGA.BR.6565.01A.11R.1802.13" "TCGA.CG.4466.01A.01R.1157.13"
## [199] "TCGA.VQ.A8PQ.01A.11R.A414.31" "TCGA.BR.8080.01A.11R.2343.13"
## [201] "TCGA.KB.A93J.01A.11R.A39E.31" "TCGA.CG.4441.01A.01R.1802.13"
## [203] "TCGA.VQ.A8DZ.01A.11R.A36D.31" "TCGA.VQ.A8PM.01A.21R.A414.31"
## [205] "TCGA.VQ.A8PP.01A.21R.A414.31" "TCGA.D7.A74A.01A.11R.A32D.31"
## [207] "TCGA.D7.A6EV.01A.11R.A31P.31" "TCGA.HU.A4GX.01A.12R.A251.31"
## [209] "TCGA.3M.AB47.01A.22R.A414.31" "TCGA.VQ.A922.01A.11R.A414.31"
## [211] "TCGA.BR.4279.01A.01R.1131.13" "TCGA.RD.A8MV.01A.11R.A36D.31"
## [213] "TCGA.VQ.A91Z.01A.11R.A414.31" "TCGA.CG.4437.01A.01R.1802.13"
## [215] "TCGA.CG.5716.01A.21R.1802.13" "TCGA.BR.6802.01A.11R.1884.13"
## [217] "TCGA.BR.6563.01A.13R.2055.13" "TCGA.BR.8284.01A.11R.2343.13"
## [219] "TCGA.VQ.A8PJ.01A.11R.A414.31" "TCGA.BR.4267.01A.01R.1131.13"
## [221] "TCGA.CG.4476.01A.01R.1157.13" "TCGA.BR.6566.01A.11R.1802.13"
## [223] "TCGA.BR.A4J2.01A.21R.A251.31" "TCGA.CG.5721.01A.11R.1602.13"
## [225] "TCGA.EQ.A4SO.01A.11R.A251.31" "TCGA.FP.A4BE.01A.12R.A24K.31"
## [227] "TCGA.F1.6874.01A.11R.1884.13" "TCGA.VQ.AA6G.01A.11R.A414.31"
## [229] "TCGA.CD.A489.01A.11R.A24K.31" "TCGA.VQ.A8PB.01A.11R.A39E.31"
## [231] "TCGA.B7.A5TK.01A.12R.A36D.31" "TCGA.FP.7998.01A.11R.2203.13"
## [233] "TCGA.BR.A4J8.01A.11R.A251.31" "TCGA.BR.4366.01A.01R.1157.13"
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## [239] "TCGA.VQ.A8PK.01A.12R.A414.31" "TCGA.CD.8531.01A.11R.2343.13"
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## [243] "TCGA.HU.A4H2.01A.11R.A251.31" "TCGA.VQ.AA6F.01A.31R.A414.31"
## [245] "TCGA.R5.A7ZR.01A.11R.A354.31" "TCGA.BR.4361.01A.01R.1157.13"
## [247] "TCGA.BR.4369.01A.01R.1157.13" "TCGA.VQ.A8PE.01A.11R.A414.31"
## [249] "TCGA.CD.5801.01A.11R.1602.13" "TCGA.CD.8530.01A.11R.2343.13"
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## [253] "TCGA.BR.8381.01A.11R.2402.13" "TCGA.VQ.A8P2.01A.11R.A36D.31"
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## [259] "TCGA.BR.8588.01A.11R.2402.13" "TCGA.D7.6526.01A.11R.1802.13"
## [261] "TCGA.BR.8592.01A.11R.2402.13" "TCGA.BR.6801.01A.11R.1884.13"
## [263] "TCGA.CG.4301.01A.01R.1157.13" "TCGA.BR.7707.01A.11R.2055.13"
## [265] "TCGA.CD.8535.01A.11R.2343.13" "TCGA.CG.4443.01A.01R.1157.13"
## [267] "TCGA.IN.A6RL.01A.11R.A32D.31" "TCGA.VQ.AA6J.01A.11R.A414.31"
## [269] "TCGA.RD.A8MW.01A.11R.A36D.31" "TCGA.VQ.A91Q.01A.12R.A414.31"
## [271] "TCGA.HU.A4H0.01A.11R.A251.31" "TCGA.CD.8524.01A.11R.2343.13"
## [273] "TCGA.BR.4370.01A.01R.1157.13" "TCGA.BR.7717.01A.11R.2055.13"
## [275] "TCGA.CG.4462.01A.01R.1157.13" "TCGA.HF.7136.01A.11R.2055.13"
## [277] "TCGA.BR.8686.01A.11R.2402.13" "TCGA.D7.8579.01A.11R.2343.13"
## [279] "TCGA.BR.8484.01A.11R.2402.13" "TCGA.BR.8363.01A.11R.2343.13"
## [281] "TCGA.HF.7133.01A.11R.2055.13" "TCGA.B7.5816.01A.21R.1602.13"
## [283] "TCGA.D7.8573.01A.11R.2343.13" "TCGA.D7.6527.01A.11R.1802.13"
## [285] "TCGA.BR.4253.01A.01R.1131.13" "TCGA.RD.A7BW.01A.11R.A32D.31"
## [287] "TCGA.CG.4465.01A.01R.1157.13" "TCGA.CD.8532.01A.11R.2343.13"
## [289] "TCGA.FP.7735.01A.11R.2055.13" "TCGA.BR.7197.01A.11R.2203.13"
## [291] "TCGA.BR.8679.01A.11R.2402.13" "TCGA.VQ.AA69.01A.11R.A414.31"
## [293] "TCGA.D7.A4YX.01A.11R.A251.31" "TCGA.FP.A9TM.01A.11R.A39E.31"
## [295] "TCGA.HU.8244.01A.11R.2343.13" "TCGA.BR.8296.01A.11R.2343.13"
## [297] "TCGA.D7.6525.01A.11R.1802.13" "TCGA.CD.A4MJ.01A.11R.A251.31"
## [299] "TCGA.VQ.A94T.01A.11R.A414.31" "TCGA.BR.A4IY.01A.11R.A251.31"
## [301] "TCGA.CG.5717.01A.11R.1602.13" "TCGA.ZA.A8F6.01A.23R.A36D.31"
## [303] "TCGA.B7.A5TN.01A.21R.A31P.31" "TCGA.BR.8589.01A.11R.2402.13"
## [305] "TCGA.BR.8373.01A.11R.2343.13" "TCGA.BR.8683.01A.11R.2402.13"
## [307] "TCGA.IN.7808.01A.11R.2203.13" "TCGA.VQ.A91W.01A.11R.A414.31"
## [309] "TCGA.FP.8209.01A.11R.2343.13" "TCGA.VQ.A8PF.01A.11R.A414.31"
## [311] "TCGA.VQ.A8PX.01A.12R.A414.31" "TCGA.VQ.A91D.01A.11R.A414.31"
## [313] "TCGA.HU.A4GC.01A.12R.A251.31" "TCGA.D7.6519.01A.11R.1802.13"
## [315] "TCGA.IN.7806.01A.11R.2055.13" "TCGA.HU.A4GT.01A.21R.A251.31"
## [317] "TCGA.HU.A4H8.01A.11R.A251.31" "TCGA.CD.5813.01A.11R.1602.13"
## [319] "TCGA.BR.A4J9.01A.12R.A251.31" "TCGA.R5.A7ZE.01B.11R.A354.31"
## [321] "TCGA.CG.4460.01A.01R.1157.13" "TCGA.D7.6528.01A.11R.1802.13"
## [323] "TCGA.VQ.A8PU.01A.12R.A414.31" "TCGA.CG.4436.01A.01R.1157.13"
## [325] "TCGA.BR.6458.01A.11R.1802.13" "TCGA.VQ.A8PO.01A.11R.A414.31"
## [327] "TCGA.BR.8382.01A.11R.2402.13" "TCGA.D7.A4YV.01A.11R.A251.31"
## [329] "TCGA.CG.5719.01A.11R.1602.13" "TCGA.CD.5804.01A.12R.2055.13"
## [331] "TCGA.D7.6522.01A.11R.1802.13" "TCGA.CD.8528.01A.11R.2343.13"
## [333] "TCGA.D7.8572.01A.11R.2343.13" "TCGA.D7.6815.01A.11R.1884.13"
## [335] "TCGA.BR.4357.01A.01R.1157.13" "TCGA.BR.6453.01A.11R.1802.13"
## [337] "TCGA.VQ.A928.01A.11R.A414.31" "TCGA.D7.6520.01A.11R.1802.13"
## [339] "TCGA.CD.8533.01A.11R.2343.13" "TCGA.B7.5818.01A.11R.1602.13"
## [341] "TCGA.FP.A4BF.01A.12R.A36D.31" "TCGA.D7.6524.01A.11R.1802.13"
## [343] "TCGA.VQ.A94R.01A.11R.A414.31" "TCGA.FP.7916.01A.11R.2203.13"
## [345] "TCGA.BR.4294.01A.01R.1131.13" "TCGA.BR.4368.01A.01R.1157.13"
## [347] "TCGA.D7.6817.01A.11R.1884.13" "TCGA.BR.8384.01A.21R.2402.13"
## [349] "TCGA.BR.7723.01A.11R.2055.13" "TCGA.HJ.7597.01A.21R.2203.13"
## [351] "TCGA.KB.A93G.01A.11R.A39E.31" "TCGA.IN.8663.01A.11R.2402.13"
## [353] "TCGA.D7.A747.01A.22R.A33Y.31" "TCGA.CG.4449.01A.01R.1157.13"
## [355] "TCGA.BR.8081.01A.11R.2343.13" "TCGA.VQ.AA64.01A.11R.A414.31"
## [357] "TCGA.D7.8574.01A.13R.2343.13" "TCGA.MX.A663.01A.11R.A31P.31"
## [359] "TCGA.VQ.A91N.01A.11R.A414.31" "TCGA.HU.8238.01A.11R.2343.13"
## [361] "TCGA.BR.8483.01A.31R.2402.13" "TCGA.CG.4306.01A.01R.1157.13"
## [363] "TCGA.BR.8291.01A.11R.2343.13" "TCGA.HU.8604.01A.11R.2402.13"
## [365] "TCGA.VQ.A8P8.01A.11R.A39E.31" "TCGA.CG.4475.01A.01R.1157.13"
## [367] "TCGA.VQ.A91K.01A.11R.A414.31" "TCGA.BR.8687.01A.11R.2402.13"
## [369] "TCGA.CD.A486.01A.11R.A24K.31" "TCGA.BR.8364.01A.11R.2343.13"
## [371] "TCGA.FP.8211.01A.11R.2343.13" "TCGA.BR.8058.01A.31R.2343.13"
## [373] "TCGA.CD.8529.01A.11R.2343.13" "TCGA.BR.4363.01A.01R.1157.13"
## [375] "TCGA.D7.A6F0.01A.11R.A31P.31" "TCGA.BR.8077.01A.11R.2343.13"
## [377] "TCGA.HU.A4GU.01A.11R.A251.31" "TCGA.BR.7901.01A.11R.2203.13"
## [379] "TCGA.D7.6820.01A.11R.1884.13" "TCGA.RD.A8N6.01A.11R.A36D.31"
## [381] "TCGA.BR.8486.01A.31R.2402.13" "TCGA.CD.8536.01A.11R.2343.13"df.t.tcga.FAM86A<-df.t.tcga %>%
filter(Hugo_Symbol == 'FAM86A')
head(df.t.tcga.FAM86A)[2]## Entrez_Gene_Id
## 1 196483dim(df.t.tcga.FAM86A)## [1] 1 382#transposing
df.t.tcga.FAM86A<-df.t.tcga.FAM86A %>%
gather(Patients,FPKM,3:ncol(.))
dim(df.t.tcga.FAM86A)## [1] 380 4head(df.t.tcga.FAM86A)## Hugo_Symbol Entrez_Gene_Id Patients FPKM
## 1 FAM86A 196483 TCGA.BR.6457.01A.21R.1802.13 325.29
## 2 FAM86A 196483 TCGA.VQ.A8PD.01A.11R.A414.31 215.77
## 3 FAM86A 196483 TCGA.BR.6803.01A.11R.1884.13 346.29
## 4 FAM86A 196483 TCGA.VQ.A8E3.01A.11R.A39E.31 277.20
## 5 FAM86A 196483 TCGA.CG.5718.01A.11R.1602.13 351.14
## 6 FAM86A 196483 TCGA.VQ.A8E2.01A.11R.A36D.31 356.05df.t.tcga.FAM86A.log2<-df.t.tcga.FAM86A %>%
mutate(log2FPKM=log(FPKM,base = 2))
head(df.t.tcga.FAM86A.log2)## Hugo_Symbol Entrez_Gene_Id Patients FPKM log2FPKM
## 1 FAM86A 196483 TCGA.BR.6457.01A.21R.1802.13 325.29 8.345583
## 2 FAM86A 196483 TCGA.VQ.A8PD.01A.11R.A414.31 215.77 7.753350
## 3 FAM86A 196483 TCGA.BR.6803.01A.11R.1884.13 346.29 8.435837
## 4 FAM86A 196483 TCGA.VQ.A8E3.01A.11R.A39E.31 277.20 8.114783
## 5 FAM86A 196483 TCGA.CG.5718.01A.11R.1602.13 351.14 8.455903
## 6 FAM86A 196483 TCGA.VQ.A8E2.01A.11R.A36D.31 356.05 8.475936###############combine the 3 data to 1###########
s.gtex<-df.gtex.FAM86A.log2 %>%
mutate(data='GTEx') %>%
dplyr::select('data','log2FPKM')
head(s.gtex)## data log2FPKM
## 1 GTEx 7.813589
## 2 GTEx 7.783457
## 3 GTEx 6.928252
## 4 GTEx 7.532239
## 5 GTEx 7.421644
## 6 GTEx 7.532239dim(s.gtex)## [1] 192 2s.nor<-df.n.tcga.FAM86A.log2 %>%
mutate(data='NAT') %>%
dplyr::select('data','log2FPKM')
s.tumor<-df.t.tcga.FAM86A.log2 %>%
mutate(data='Tumor') %>%
dplyr::select('data','log2FPKM')
#binding rows
unify.FAM86A<-rbind(s.gtex,s.nor,s.tumor)
head(unify.FAM86A)## data log2FPKM
## 1 GTEx 7.813589
## 2 GTEx 7.783457
## 3 GTEx 6.928252
## 4 GTEx 7.532239
## 5 GTEx 7.421644
## 6 GTEx 7.532239dim(unify.FAM86A)## [1] 605 2View(unify.FAM86A)
count(unify.FAM86A,data)## data n
## 1 GTEx 192
## 2 NAT 33
## 3 Tumor 380
##
## Kruskal-Wallis rank sum test
##
## data: log2FPKM by source
## Kruskal-Wallis chi-squared = 55.539, df = 2, p-value = 8.706e-13##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: a$log2FPKM and a$source
##
## GTEx Normal TCGA
## Normal TCGA 0.63 -
## Tumor TCGA 2.1e-11 8.9e-05
##
## P value adjustment method: BHTCGA analysis for subtype expression
####IMPORTANT! Please download the github version to use the most recent version of TCGAbiolinks
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks",force = TRUE)## magrittr (2.0.1 -> 2.0.3 ) [CRAN]
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## * checking for file 'C:\Users\nuraz\AppData\Local\Temp\RtmpYDVDl6\remotes34bc49f643d7\BioinformaticsFMRP-TCGAbiolinks-3140986/DESCRIPTION' ... OK
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## * building 'TCGAbiolinks_2.7.9.tar.gz'
## library(TCGAbiolinks)
library(SummarizedExperiment)
library(recount)
###conversion of uuids to TCGA barcodes
library(TCGAutils)
library(limma)
library(biomaRt)
query <- GDCquery(project = "TCGA-STAD",
data.category = "Gene expression",
data.type = "Gene expression quantification",
platform = "Illumina HiSeq",
file.type = "results",
legacy = TRUE,
sample.type = c("Primary Tumor"))
GDCdownload(query)
stad.exp<-GDCprepare(query,
save = TRUE,
summarizedExperiment = TRUE,
save.filename = "STADIllumina_HiSeq.rda")##
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|====================================================|100% Completed after 44 shead(stad.exp)## class: RangedSummarizedExperiment
## dim: 6 415
## metadata(1): data_release
## assays(2): raw_count scaled_estimate
## rownames(6): A1BG|1 A2M|2 ... SERPINA3|12 AADAC|13
## rowData names(4): gene_id entrezgene ensembl_gene_id
## transcript_id.transcript_id_TCGA-CD-8536-01A-11R-2343-13
## colnames(415): TCGA-CD-8536-01A-11R-2343-13
## TCGA-BR-8077-01A-11R-2343-13 ... TCGA-VQ-A8PQ-01A-11R-A414-31
## TCGA-CD-8535-01A-11R-2343-13
## colData names(109): barcode patient ... paper_CIMP.Category
## paper_stringAsFactorrse <- get(load("STADIllumina_HiSeq.rda"))
dataClin_STAD <- GDCquery_clinic("TCGA-STAD", "Clinical")
write.csv(dataClin_STAD, "dataClin_STAD.csv")
dataPrep_STAD<-TCGAanalyze_Preprocessing(rse,
cor.cut = .5,
datatype = "raw_count",
filename = "STAD_IlluminaHiSeq_RNASeqV2.png")# normalization of genes
dataNorm<-TCGAanalyze_Normalization(tabDF = dataPrep_STAD,geneInfo = geneInfo,method = "gcContent")
head(dataNorm)## TCGA-3M-AB46-01A-11R-A414-31 TCGA-3M-AB47-01A-22R-A414-31
## 100133144 37 36
## 100134869 50 18
## 155060 555 387
## 280660 0 0
## 8225 990 1502
## 90288 33 6
## TCGA-B7-5816-01A-21R-1602-13 TCGA-B7-5818-01A-11R-1602-13
## 100133144 16 38
## 100134869 54 247
## 155060 105 333
## 280660 0 0
## 8225 996 1314
## 90288 5 32
## TCGA-B7-A5TI-01A-11R-A31P-31 TCGA-B7-A5TJ-01A-11R-A31P-31
## 100133144 39 106
## 100134869 53 87
## 155060 179 880
## 280660 0 0
## 8225 1584 2202
## 90288 4 0
## TCGA-B7-A5TK-01A-12R-A36D-31 TCGA-B7-A5TN-01A-21R-A31P-31
## 100133144 19 57
## 100134869 0 56
## 155060 134 147
## 280660 0 0
## 8225 875 708
## 90288 21 7
## TCGA-BR-4187-01A-01R-1131-13 TCGA-BR-4191-01A-02R-1131-13
## 100133144 6 36
## 100134869 2 28
## 155060 70 455
## 280660 0 0
## 8225 914 742
## 90288 0 2
## TCGA-BR-4201-01A-01R-1131-13 TCGA-BR-4253-01A-01R-1131-13
## 100133144 31 27
## 100134869 11 35
## 155060 358 499
## 280660 0 0
## 8225 688 1217
## 90288 10 23
## TCGA-BR-4255-01A-01R-1131-13 TCGA-BR-4256-01A-01R-1131-13
## 100133144 0 5
## 100134869 15 21
## 155060 68 153
## 280660 0 0
## 8225 866 1061
## 90288 15 6
## TCGA-BR-4257-01A-01R-1131-13 TCGA-BR-4267-01A-01R-1131-13
## 100133144 92 51
## 100134869 21 59
## 155060 265 309
## 280660 0 0
## 8225 829 1152
## 90288 3 50
## TCGA-BR-4279-01A-01R-1131-13 TCGA-BR-4280-01A-01R-1131-13
## 100133144 2 98
## 100134869 1 82
## 155060 76 492
## 280660 0 0
## 8225 677 1174
## 90288 7 0
## TCGA-BR-4292-01A-01R-1131-13 TCGA-BR-4294-01A-01R-1131-13
## 100133144 134 142
## 100134869 63 30
## 155060 330 142
## 280660 0 0
## 8225 1399 783
## 90288 38 608
## TCGA-BR-4357-01A-01R-1157-13 TCGA-BR-4361-01A-01R-1157-13
## 100133144 27 120
## 100134869 24 19
## 155060 405 729
## 280660 2 0
## 8225 1631 1644
## 90288 45 14
## TCGA-BR-4362-01A-01R-1157-13 TCGA-BR-4363-01A-01R-1157-13
## 100133144 107 57
## 100134869 38 27
## 155060 509 415
## 280660 0 0
## 8225 1419 1542
## 90288 5 1
## TCGA-BR-4366-01A-01R-1157-13 TCGA-BR-4367-01A-01R-1157-13
## 100133144 21 30
## 100134869 14 38
## 155060 510 131
## 280660 0 0
## 8225 1962 474
## 90288 9 3
## TCGA-BR-4368-01A-01R-1157-13 TCGA-BR-4369-01A-01R-1157-13
## 100133144 113 38
## 100134869 17 14
## 155060 596 583
## 280660 0 0
## 8225 1329 585
## 90288 12 4
## TCGA-BR-4370-01A-01R-1157-13 TCGA-BR-4371-01A-01R-1157-13
## 100133144 43 118
## 100134869 32 55
## 155060 405 693
## 280660 0 0
## 8225 691 1477
## 90288 24 2
## TCGA-BR-6452-01A-12R-1802-13 TCGA-BR-6453-01A-11R-1802-13
## 100133144 100 34
## 100134869 60 58
## 155060 203 94
## 280660 0 0
## 8225 881 1333
## 90288 27 7
## TCGA-BR-6454-01A-11R-1802-13 TCGA-BR-6455-01A-11R-1802-13
## 100133144 49 113
## 100134869 60 34
## 155060 149 190
## 280660 0 0
## 8225 481 1687
## 90288 18 3
## TCGA-BR-6456-01A-11R-1802-13 TCGA-BR-6457-01A-21R-1802-13
## 100133144 29 11
## 100134869 25 25
## 155060 116 96
## 280660 0 0
## 8225 824 920
## 90288 4 7
## TCGA-BR-6458-01A-11R-1802-13 TCGA-BR-6563-01A-13R-2055-13
## 100133144 103 8
## 100134869 77 26
## 155060 199 87
## 280660 0 0
## 8225 697 1427
## 90288 17 13
## TCGA-BR-6564-01A-12R-1884-13 TCGA-BR-6565-01A-11R-1802-13
## 100133144 14 32
## 100134869 41 62
## 155060 138 271
## 280660 0 0
## 8225 1107 813
## 90288 13 6
## TCGA-BR-6566-01A-11R-1802-13 TCGA-BR-6705-01A-12R-1884-13
## 100133144 62 19
## 100134869 59 13
## 155060 88 187
## 280660 0 0
## 8225 1250 993
## 90288 3 17
## TCGA-BR-6706-01A-11R-1884-13 TCGA-BR-6707-01A-11R-1884-13
## 100133144 25 96
## 100134869 29 112
## 155060 448 296
## 280660 0 0
## 8225 1068 980
## 90288 10 27
## TCGA-BR-6709-01A-11R-1884-13 TCGA-BR-6801-01A-11R-1884-13
## 100133144 5 49
## 100134869 32 22
## 155060 190 310
## 280660 0 0
## 8225 1531 1293
## 90288 9 0
## TCGA-BR-6802-01A-11R-1884-13 TCGA-BR-6803-01A-11R-1884-13
## 100133144 26 16
## 100134869 27 15
## 155060 239 84
## 280660 0 0
## 8225 1374 1172
## 90288 4 9
## TCGA-BR-6852-01A-11R-1884-13 TCGA-BR-7196-01A-11R-2055-13
## 100133144 55 48
## 100134869 70 46
## 155060 178 215
## 280660 0 0
## 8225 999 1085
## 90288 5 18
## TCGA-BR-7197-01A-11R-2203-13 TCGA-BR-7703-01A-11R-2055-13
## 100133144 115 161
## 100134869 112 205
## 155060 342 388
## 280660 0 0
## 8225 1344 2059
## 90288 3 12
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## 8225 1259 2068
## 90288 13 29
## TCGA-D7-A6F0-01A-11R-A31P-31 TCGA-D7-A6F2-01A-12R-A31P-31
## 100133144 30 101
## 100134869 22 88
## 155060 170 851
## 280660 0 0
## 8225 1643 1086
## 90288 55 2
## TCGA-D7-A747-01A-22R-A33Y-31 TCGA-D7-A748-01A-12R-A32D-31
## 100133144 29 0
## 100134869 12 8
## 155060 345 80
## 280660 0 0
## 8225 1242 859
## 90288 8 2
## TCGA-D7-A74A-01A-11R-A32D-31 TCGA-EQ-8122-01A-11R-2343-13
## 100133144 70 59
## 100134869 88 30
## 155060 210 260
## 280660 0 0
## 8225 795 476
## 90288 43 3
## TCGA-EQ-A4SO-01A-11R-A251-31 TCGA-F1-6177-01A-11R-1802-13
## 100133144 40 229
## 100134869 52 104
## 155060 242 853
## 280660 0 0
## 8225 1836 1501
## 90288 44 21
## TCGA-F1-6874-01A-11R-1884-13 TCGA-F1-6875-01A-11R-2055-13
## 100133144 117 236
## 100134869 50 272
## 155060 224 542
## 280660 0 0
## 8225 1055 783
## 90288 20 9
## TCGA-F1-A448-01A-11R-A24K-31 TCGA-F1-A72C-01A-21R-A33Y-31
## 100133144 92 20
## 100134869 58 141
## 155060 277 232
## 280660 0 0
## 8225 1308 500
## 90288 8 184
## TCGA-FP-7735-01A-11R-2055-13 TCGA-FP-7829-01A-11R-2055-13
## 100133144 5 110
## 100134869 14 94
## 155060 149 122
## 280660 0 0
## 8225 899 1279
## 90288 17 7
## TCGA-FP-7916-01A-11R-2203-13 TCGA-FP-7998-01A-11R-2203-13
## 100133144 43 36
## 100134869 51 31
## 155060 390 290
## 280660 0 0
## 8225 855 1189
## 90288 6 8
## TCGA-FP-8099-01A-11R-2343-13 TCGA-FP-8209-01A-11R-2343-13
## 100133144 137 12
## 100134869 110 21
## 155060 427 498
## 280660 0 0
## 8225 635 996
## 90288 4 9
## TCGA-FP-8210-01A-11R-2343-13 TCGA-FP-8211-01A-11R-2343-13
## 100133144 34 116
## 100134869 10 105
## 155060 240 256
## 280660 0 0
## 8225 842 1660
## 90288 15 4
## TCGA-FP-8631-01A-11R-2402-13 TCGA-FP-A4BE-01A-12R-A24K-31
## 100133144 100 101
## 100134869 146 84
## 155060 155 266
## 280660 0 0
## 8225 1125 1667
## 90288 11 46
## TCGA-FP-A4BF-01A-12R-A36D-31 TCGA-FP-A8CX-01A-11R-A36D-31
## 100133144 40 105
## 100134869 14 125
## 155060 506 315
## 280660 0 0
## 8225 1072 1398
## 90288 6 16
## TCGA-FP-A9TM-01A-11R-A39E-31 TCGA-HF-7131-01A-11R-2055-13
## 100133144 100 21
## 100134869 73 40
## 155060 634 147
## 280660 0 0
## 8225 1699 865
## 90288 26 40
## TCGA-HF-7132-01A-11R-2055-13 TCGA-HF-7133-01A-11R-2055-13
## 100133144 48 59
## 100134869 74 84
## 155060 190 185
## 280660 0 0
## 8225 799 1274
## 90288 8 2
## TCGA-HF-7134-01A-11R-2055-13 TCGA-HF-7136-01A-11R-2055-13
## 100133144 103 52
## 100134869 90 76
## 155060 312 238
## 280660 0 0
## 8225 380 1882
## 90288 7 3
## TCGA-HF-A5NB-01A-11R-A31P-31 TCGA-HJ-7597-01A-21R-2203-13
## 100133144 128 110
## 100134869 104 131
## 155060 646 288
## 280660 0 0
## 8225 1159 1122
## 90288 5 5
## TCGA-HU-8238-01A-11R-2343-13 TCGA-HU-8243-01A-11R-2343-13
## 100133144 75 31
## 100134869 108 71
## 155060 137 300
## 280660 0 0
## 8225 893 1080
## 90288 19 9
## TCGA-HU-8244-01A-11R-2343-13 TCGA-HU-8249-01A-11R-A36D-31
## 100133144 154 42
## 100134869 174 50
## 155060 423 344
## 280660 0 0
## 8225 1410 1594
## 90288 2 0
## TCGA-HU-8602-01A-11R-2402-13 TCGA-HU-8604-01A-11R-2402-13
## 100133144 185 28
## 100134869 162 69
## 155060 324 318
## 280660 0 0
## 8225 1166 2038
## 90288 79 2
## TCGA-HU-8608-01A-11R-2402-13 TCGA-HU-8610-01A-22R-2402-13
## 100133144 78 81
## 100134869 62 67
## 155060 178 403
## 280660 0 0
## 8225 1417 283
## 90288 74 42
## TCGA-HU-A4G2-01A-11R-A251-31 TCGA-HU-A4G3-01A-11R-A24K-31
## 100133144 131 154
## 100134869 50 74
## 155060 305 410
## 280660 0 0
## 8225 816 613
## 90288 54 86
## TCGA-HU-A4G6-01A-11R-A24K-31 TCGA-HU-A4G8-01A-11R-A251-31
## 100133144 233 250
## 100134869 187 76
## 155060 288 374
## 280660 0 0
## 8225 1258 1906
## 90288 148 32
## TCGA-HU-A4G9-01A-11R-A24K-31 TCGA-HU-A4GC-01A-12R-A251-31
## 100133144 365 187
## 100134869 211 36
## 155060 519 182
## 280660 0 0
## 8225 2016 1375
## 90288 52 4
## TCGA-HU-A4GD-01A-11R-A36D-31 TCGA-HU-A4GF-01A-11R-A24K-31
## 100133144 13 83
## 100134869 16 51
## 155060 673 336
## 280660 0 0
## 8225 2466 1687
## 90288 19 102
## TCGA-HU-A4GH-01A-11R-A24K-31 TCGA-HU-A4GJ-01A-11R-A251-31
## 100133144 138 102
## 100134869 61 43
## 155060 359 627
## 280660 0 0
## 8225 1025 1323
## 90288 6 38
## TCGA-HU-A4GN-01A-11R-A251-31 TCGA-HU-A4GP-01A-11R-A251-31
## 100133144 215 128
## 100134869 157 75
## 155060 465 327
## 280660 0 0
## 8225 1335 970
## 90288 38 35
## TCGA-HU-A4GQ-01A-11R-A36D-31 TCGA-HU-A4GT-01A-21R-A251-31
## 100133144 65 116
## 100134869 50 66
## 155060 247 303
## 280660 0 0
## 8225 1094 1607
## 90288 5 22
## TCGA-HU-A4GU-01A-11R-A251-31 TCGA-HU-A4GX-01A-12R-A251-31
## 100133144 190 181
## 100134869 111 81
## 155060 311 413
## 280660 0 0
## 8225 637 1656
## 90288 6 14
## TCGA-HU-A4GY-01A-21R-A24K-31 TCGA-HU-A4H0-01A-11R-A251-31
## 100133144 71 143
## 100134869 35 71
## 155060 693 634
## 280660 0 0
## 8225 1126 1067
## 90288 10 75
## TCGA-HU-A4H2-01A-11R-A251-31 TCGA-HU-A4H3-01A-21R-A251-31
## 100133144 269 201
## 100134869 178 114
## 155060 178 606
## 280660 0 0
## 8225 2820 1388
## 90288 68 51
## TCGA-HU-A4H4-01A-21R-A251-31 TCGA-HU-A4H5-01A-21R-A251-31
## 100133144 123 38
## 100134869 58 63
## 155060 231 279
## 280660 0 0
## 8225 858 1007
## 90288 47 37
## TCGA-HU-A4H6-01A-11R-A251-31 TCGA-HU-A4H8-01A-11R-A251-31
## 100133144 560 304
## 100134869 90 122
## 155060 176 899
## 280660 0 3
## 8225 1374 1165
## 90288 13 20
## TCGA-HU-A4HB-01A-12R-A251-31 TCGA-HU-A4HD-01A-11R-A251-31
## 100133144 50 76
## 100134869 53 70
## 155060 260 216
## 280660 0 0
## 8225 859 1246
## 90288 11 16
## TCGA-IN-7806-01A-11R-2055-13 TCGA-IN-7808-01A-11R-2203-13
## 100133144 150 104
## 100134869 86 107
## 155060 719 750
## 280660 0 0
## 8225 1178 1123
## 90288 4 3
## TCGA-IN-8462-01A-11R-2343-13 TCGA-IN-8663-01A-11R-2402-13
## 100133144 96 214
## 100134869 56 122
## 155060 157 380
## 280660 0 0
## 8225 723 312
## 90288 10 3
## TCGA-IN-A6RI-01A-11R-A32D-31 TCGA-IN-A6RJ-01A-21R-A33Y-31
## 100133144 33 351
## 100134869 62 381
## 155060 117 387
## 280660 106 0
## 8225 1918 1305
## 90288 49 0
## TCGA-IN-A6RL-01A-11R-A32D-31 TCGA-IN-A6RN-01A-12R-A33Y-31
## 100133144 81 99
## 100134869 63 136
## 155060 138 298
## 280660 0 0
## 8225 1161 1401
## 90288 1 12
## TCGA-IN-A6RO-01A-12R-A33Y-31 TCGA-IN-A6RR-01A-12R-A32D-31
## 100133144 131 29
## 100134869 128 60
## 155060 350 188
## 280660 0 0
## 8225 953 1799
## 90288 12 2
## TCGA-IN-A6RS-01A-12R-A354-31 TCGA-IN-A7NR-01A-11R-A354-31
## 100133144 63 143
## 100134869 27 196
## 155060 208 156
## 280660 0 0
## 8225 729 989
## 90288 5 0
## TCGA-IN-A7NT-01A-21R-A354-31 TCGA-IN-A7NU-01A-22R-A354-31
## 100133144 45 16
## 100134869 85 33
## 155060 286 153
## 280660 0 0
## 8225 1151 826
## 90288 35 13
## TCGA-IN-AB1V-01A-21R-A414-31 TCGA-IN-AB1X-01A-11R-A39E-31
## 100133144 263 135
## 100134869 273 67
## 155060 446 365
## 280660 0 0
## 8225 1385 971
## 90288 23 29
## TCGA-IP-7968-01A-11R-2203-13 TCGA-KB-A6F7-01A-12R-A32D-31
## 100133144 26 54
## 100134869 30 36
## 155060 468 219
## 280660 0 20
## 8225 680 1184
## 90288 60 16
## TCGA-KB-A93G-01A-11R-A39E-31 TCGA-KB-A93H-01A-11R-A39E-31
## 100133144 77 159
## 100134869 22 118
## 155060 474 341
## 280660 0 0
## 8225 1023 2856
## 90288 2 18
## TCGA-KB-A93J-01A-11R-A39E-31 TCGA-MX-A5UG-01A-21R-A31P-31
## 100133144 60 30
## 100134869 57 11
## 155060 338 482
## 280660 0 0
## 8225 1647 1190
## 90288 11 11
## TCGA-MX-A5UJ-01A-11R-A31P-31 TCGA-MX-A663-01A-11R-A31P-31
## 100133144 87 6
## 100134869 47 6
## 155060 329 240
## 280660 0 0
## 8225 1045 764
## 90288 6 11
## TCGA-MX-A666-01A-11R-A31P-31 TCGA-R5-A7O7-01A-11R-A33Y-31
## 100133144 23 55
## 100134869 16 83
## 155060 554 266
## 280660 0 0
## 8225 1031 1852
## 90288 8 85
## TCGA-R5-A7ZE-01B-11R-A354-31 TCGA-R5-A7ZF-01A-11R-A354-31
## 100133144 81 53
## 100134869 57 45
## 155060 164 295
## 280660 0 2
## 8225 1466 1376
## 90288 10 17
## TCGA-R5-A7ZI-01A-11R-A354-31 TCGA-R5-A7ZR-01A-11R-A354-31
## 100133144 84 30
## 100134869 93 30
## 155060 389 137
## 280660 0 0
## 8225 2202 2510
## 90288 19 6
## TCGA-R5-A805-01A-11R-A36D-31 TCGA-RD-A7BS-01A-11R-A32D-31
## 100133144 98 67
## 100134869 138 31
## 155060 228 140
## 280660 0 0
## 8225 722 655
## 90288 19 4
## TCGA-RD-A7BT-01A-11R-A33Y-31 TCGA-RD-A7BW-01A-11R-A32D-31
## 100133144 116 13
## 100134869 108 21
## 155060 402 284
## 280660 0 0
## 8225 1202 795
## 90288 6 0
## TCGA-RD-A7C1-01A-11R-A32D-31 TCGA-RD-A8MV-01A-11R-A36D-31
## 100133144 0 53
## 100134869 18 91
## 155060 326 476
## 280660 0 0
## 8225 628 831
## 90288 0 8
## TCGA-RD-A8MW-01A-11R-A36D-31 TCGA-RD-A8N0-01A-12R-A36D-31
## 100133144 17 102
## 100134869 20 47
## 155060 126 382
## 280660 0 0
## 8225 1605 1416
## 90288 11 8
## TCGA-RD-A8N1-01A-12R-A36D-31 TCGA-RD-A8N2-01A-12R-A36D-31
## 100133144 53 29
## 100134869 25 16
## 155060 551 726
## 280660 0 0
## 8225 1837 1342
## 90288 9 12
## TCGA-RD-A8N4-01A-21R-A36D-31 TCGA-RD-A8N5-01A-12R-A36D-31
## 100133144 69 69
## 100134869 20 23
## 155060 408 475
## 280660 0 0
## 8225 727 835
## 90288 48 31
## TCGA-RD-A8N6-01A-11R-A36D-31 TCGA-RD-A8N9-01A-12R-A39E-31
## 100133144 53 39
## 100134869 23 23
## 155060 203 349
## 280660 0 2
## 8225 652 1327
## 90288 12 16
## TCGA-RD-A8NB-01A-12R-A39E-31 TCGA-SW-A7EA-01A-12R-A354-31
## 100133144 57 78
## 100134869 26 51
## 155060 344 252
## 280660 0 0
## 8225 1308 1200
## 90288 9 13
## TCGA-SW-A7EB-01A-11R-A354-31 TCGA-VQ-A8DT-01A-11R-A36D-31
## 100133144 25 63
## 100134869 24 31
## 155060 116 368
## 280660 0 0
## 8225 1108 2047
## 90288 14 72
## TCGA-VQ-A8DU-01A-11R-A36D-31 TCGA-VQ-A8DV-01A-12R-A36D-31
## 100133144 19 11
## 100134869 61 10
## 155060 274 428
## 280660 0 0
## 8225 1224 1760
## 90288 29 22
## TCGA-VQ-A8DZ-01A-11R-A36D-31 TCGA-VQ-A8E0-01A-11R-A414-31
## 100133144 39 51
## 100134869 64 19
## 155060 165 158
## 280660 0 0
## 8225 923 2299
## 90288 4 56
## TCGA-VQ-A8E2-01A-11R-A36D-31 TCGA-VQ-A8E3-01A-11R-A39E-31
## 100133144 44 56
## 100134869 51 32
## 155060 425 430
## 280660 0 0
## 8225 1371 845
## 90288 51 11
## TCGA-VQ-A8E7-01B-11R-A414-31 TCGA-VQ-A8P2-01A-11R-A36D-31
## 100133144 93 118
## 100134869 45 102
## 155060 312 432
## 280660 0 0
## 8225 1624 1809
## 90288 17 16
## TCGA-VQ-A8P3-01A-11R-A36D-31 TCGA-VQ-A8P5-01A-11R-A39E-31
## 100133144 35 97
## 100134869 78 40
## 155060 300 283
## 280660 7 0
## 8225 841 1770
## 90288 92 10
## TCGA-VQ-A8P8-01A-11R-A39E-31 TCGA-VQ-A8PB-01A-11R-A39E-31
## 100133144 24 116
## 100134869 22 72
## 155060 222 408
## 280660 0 0
## 8225 1172 1829
## 90288 23 17
## TCGA-VQ-A8PC-01A-11R-A39E-31 TCGA-VQ-A8PD-01A-11R-A414-31
## 100133144 100 50
## 100134869 33 28
## 155060 318 632
## 280660 0 0
## 8225 683 1418
## 90288 14 10
## TCGA-VQ-A8PE-01A-11R-A414-31 TCGA-VQ-A8PF-01A-11R-A414-31
## 100133144 39 54
## 100134869 15 35
## 155060 318 425
## 280660 0 0
## 8225 2582 1683
## 90288 4 9
## TCGA-VQ-A8PH-01A-12R-A414-31 TCGA-VQ-A8PJ-01A-11R-A414-31
## 100133144 124 74
## 100134869 44 32
## 155060 435 146
## 280660 0 0
## 8225 622 1394
## 90288 11 30
## TCGA-VQ-A8PK-01A-12R-A414-31 TCGA-VQ-A8PM-01A-21R-A414-31
## 100133144 56 54
## 100134869 22 23
## 155060 186 272
## 280660 0 0
## 8225 1648 3070
## 90288 28 13
## TCGA-VQ-A8PO-01A-11R-A414-31 TCGA-VQ-A8PP-01A-21R-A414-31
## 100133144 72 152
## 100134869 34 76
## 155060 303 647
## 280660 0 0
## 8225 2396 1803
## 90288 18 0
## TCGA-VQ-A8PQ-01A-11R-A414-31 TCGA-VQ-A8PU-01A-12R-A414-31
## 100133144 42 71
## 100134869 32 52
## 155060 590 513
## 280660 0 0
## 8225 1385 1057
## 90288 11 61
## TCGA-VQ-A8PX-01A-12R-A414-31 TCGA-VQ-A91A-01A-11R-A414-31
## 100133144 167 33
## 100134869 91 34
## 155060 506 782
## 280660 0 0
## 8225 2196 978
## 90288 20 6
## TCGA-VQ-A91D-01A-11R-A414-31 TCGA-VQ-A91E-01A-31R-A414-31
## 100133144 210 191
## 100134869 106 91
## 155060 976 638
## 280660 0 0
## 8225 1507 1507
## 90288 43 151
## TCGA-VQ-A91K-01A-11R-A414-31 TCGA-VQ-A91N-01A-11R-A414-31
## 100133144 122 120
## 100134869 57 52
## 155060 364 390
## 280660 0 0
## 8225 1365 1539
## 90288 13 51
## TCGA-VQ-A91Q-01A-12R-A414-31 TCGA-VQ-A91S-01A-11R-A414-31
## 100133144 102 83
## 100134869 72 17
## 155060 370 408
## 280660 0 0
## 8225 1287 1288
## 90288 12 43
## TCGA-VQ-A91U-01A-11R-A414-31 TCGA-VQ-A91V-01A-11R-A414-31
## 100133144 50 130
## 100134869 54 54
## 155060 548 561
## 280660 0 0
## 8225 1478 1334
## 90288 5 68
## TCGA-VQ-A91W-01A-11R-A414-31 TCGA-VQ-A91X-01A-12R-A414-31
## 100133144 139 134
## 100134869 103 48
## 155060 471 858
## 280660 0 0
## 8225 1670 1859
## 90288 77 16
## TCGA-VQ-A91Y-01A-11R-A414-31 TCGA-VQ-A91Z-01A-11R-A414-31
## 100133144 35 108
## 100134869 15 86
## 155060 431 608
## 280660 0 0
## 8225 761 530
## 90288 5 197
## TCGA-VQ-A922-01A-11R-A414-31 TCGA-VQ-A923-01A-11R-A414-31
## 100133144 112 131
## 100134869 52 67
## 155060 423 1096
## 280660 0 0
## 8225 627 1120
## 90288 16 19
## TCGA-VQ-A924-01A-11R-A414-31 TCGA-VQ-A925-01A-11R-A414-31
## 100133144 137 76
## 100134869 68 57
## 155060 396 506
## 280660 0 0
## 8225 1605 2319
## 90288 1 176
## TCGA-VQ-A927-01A-12R-A414-31 TCGA-VQ-A928-01A-11R-A414-31
## 100133144 97 92
## 100134869 48 53
## 155060 444 780
## 280660 0 0
## 8225 1506 1407
## 90288 23 481
## TCGA-VQ-A92D-01A-11R-A414-31 TCGA-VQ-A94O-01A-11R-A414-31
## 100133144 113 56
## 100134869 110 49
## 155060 263 338
## 280660 0 0
## 8225 641 1074
## 90288 38 42
## TCGA-VQ-A94P-01A-13R-A414-31 TCGA-VQ-A94R-01A-11R-A414-31
## 100133144 38 146
## 100134869 15 50
## 155060 270 607
## 280660 0 1
## 8225 1426 1331
## 90288 2 24
## TCGA-VQ-A94T-01A-11R-A414-31 TCGA-VQ-A94U-01A-12R-A414-31
## 100133144 89 79
## 100134869 81 64
## 155060 358 608
## 280660 0 0
## 8225 808 1279
## 90288 18 27
## TCGA-VQ-AA64-01A-11R-A414-31 TCGA-VQ-AA68-01A-11R-A414-31
## 100133144 74 104
## 100134869 55 78
## 155060 259 296
## 280660 0 0
## 8225 879 775
## 90288 132 15
## TCGA-VQ-AA69-01A-11R-A414-31 TCGA-VQ-AA6A-01A-11R-A414-31
## 100133144 255 83
## 100134869 152 39
## 155060 628 481
## 280660 0 0
## 8225 1437 896
## 90288 13 41
## TCGA-VQ-AA6B-01A-11R-A414-31 TCGA-VQ-AA6D-01A-11R-A414-31
## 100133144 128 117
## 100134869 72 73
## 155060 948 435
## 280660 0 0
## 8225 2559 3326
## 90288 13 10
## TCGA-VQ-AA6F-01A-31R-A414-31 TCGA-VQ-AA6G-01A-11R-A414-31
## 100133144 54 154
## 100134869 42 84
## 155060 370 270
## 280660 0 0
## 8225 1049 964
## 90288 244 9
## TCGA-VQ-AA6I-01A-11R-A414-31 TCGA-VQ-AA6J-01A-11R-A414-31
## 100133144 132 72
## 100134869 98 48
## 155060 228 214
## 280660 0 0
## 8225 2356 1448
## 90288 21 27
## TCGA-VQ-AA6K-01A-11R-A414-31 TCGA-ZA-A8F6-01A-23R-A36D-31
## 100133144 76 55
## 100134869 51 30
## 155060 539 337
## 280660 0 0
## 8225 1810 1638
## 90288 52 7
## TCGA-ZQ-A9CR-01A-11R-A39E-31
## 100133144 65
## 100134869 25
## 155060 205
## 280660 0
## 8225 960
## 90288 12# quantile filter of genes
dataFilt <- TCGAanalyze_Filtering(tabDF = dataNorm,
method = "quantile",
qnt.cut = 0.25)
write.csv(dataFilt,"dataFilt TCGA only tumor.csv")
#check clinical
rse$age_at_index## [1] 74 58 54 53 53 67 56 59 70 78 75 86 59 81 69 78 75 70 71 67 41 82 56 53 66
## [26] 60 62 57 63 78 76 63 78 63 67 75 53 59 74 73 84 65 75 68 57 65 58 83 64 76
## [51] 72 76 64 55 64 72 62 61 73 63 66 62 45 87 68 62 70 49 69 62 45 69 69 54 68
## [76] 49 80 64 69 82 75 66 49 69 57 39 59 68 82 77 49 70 76 72 51 66 60 65 47 59
## [101] 79 68 69 79 62 52 58 72 71 51 51 72 70 69 63 72 67 83 50 51 78 58 62 70 50
## [126] 54 60 78 67 76 74 70 71 NA 72 58 57 60 70 71 61 71 79 76 73 46 77 62 71 54
## [151] 63 68 53 62 65 53 76 66 75 58 67 70 72 70 43 53 57 79 71 44 58 51 60 69 74
## [176] 48 58 78 81 72 86 90 51 55 56 65 58 54 86 48 68 52 80 71 79 74 75 76 66 69
## [201] 57 76 65 70 69 70 69 74 70 79 49 78 67 54 68 66 41 70 60 68 NA 72 71 63 65
## [226] 64 75 74 73 77 58 61 66 57 69 72 84 68 71 68 61 75 63 62 63 61 56 61 67 56
## [251] 68 57 80 58 77 64 56 72 56 56 73 69 81 78 42 90 59 78 63 79 59 51 74 73 60
## [276] NA 80 73 77 67 66 68 70 90 60 68 68 75 70 72 82 35 84 80 34 74 65 57 56 65
## [301] 58 69 76 72 90 68 72 57 64 66 74 79 48 70 54 65 78 72 67 55 76 53 72 52 67
## [326] 45 83 57 59 67 55 79 43 68 79 69 66 74 70 71 72 45 55 58 63 73 78 67 72 71
## [351] 59 45 66 72 74 73 59 64 61 58 45 56 59 58 78 57 69 51 30 68 75 70 53 65 NA
## [376] 69 52 51 51 74 84 74 NA 70 52 71 70 77 62 48 61 60 46 43 71 61 85 77 75 60
## [401] 80 58 70 63 81 77 63 68 58 51 56 90 44 50 59rse$definition## [1] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [4] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [7] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [10] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [13] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [16] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [19] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [22] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [25] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [28] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [31] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [34] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [37] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [40] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [43] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [46] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [49] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [52] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [55] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [58] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [61] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [64] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [67] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [70] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [73] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [76] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [79] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [82] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [85] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [88] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [91] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [94] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [97] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [100] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [103] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [106] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [109] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [112] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [115] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [118] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [121] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [124] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [127] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [130] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [133] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [136] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [139] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [142] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [145] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [148] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [151] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [154] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [157] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [160] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [163] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [166] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [169] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [172] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [175] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [178] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [181] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [184] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [187] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [190] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [193] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [196] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [199] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [202] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [205] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [208] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [211] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [214] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [217] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [220] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [223] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [226] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [229] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [232] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [235] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [238] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [241] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [244] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [247] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [250] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [253] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [256] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [259] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [262] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [265] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [268] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [271] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [274] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [277] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [280] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [283] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [286] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [289] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [292] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [295] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [298] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [301] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [304] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [307] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [310] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [313] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [316] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [319] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [322] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [325] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [328] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [331] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [334] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [337] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [340] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [343] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [346] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [349] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [352] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [355] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [358] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [361] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [364] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [367] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [370] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [373] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [376] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [379] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [382] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [385] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [388] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [391] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [394] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [397] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [400] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [403] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [406] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [409] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [412] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [415] "Primary solid Tumor"rse$days_to_diagnosis## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [26] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [51] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [76] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [101] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [126] 0 0 0 0 0 0 0 0 NA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [151] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [176] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [201] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA 0 0 0 0
## [226] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [251] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [276] NA 0 0 0 0 0 0 0 0 0 0 0 NA 0 0 0 0 0 0 0 0 0 0 0 0
## [301] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [326] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [351] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA
## [376] 0 0 0 0 0 0 0 NA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [401] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0rse$ajcc_pathologic_stage## [1] "Stage II" "Stage IIIB" "Stage IIB" "Stage IIB" "Stage IIIB"
## [6] "Stage IV" "Stage IIIC" "Stage IIB" "Stage IIIC" "Stage IIA"
## [11] "Stage IIIB" "Stage IIIA" "Stage IIIB" "Stage II" "Stage II"
## [16] NA "Stage IIIB" "Stage IIB" NA "Stage IIIB"
## [21] "Stage IV" "Stage II" NA "Stage IIIB" "Stage IIIA"
## [26] "Stage IIIB" "Stage IB" "Stage IIB" "Stage IIIB" "Stage IIIA"
## [31] "Stage IIB" "Stage IIIA" "Stage IIIA" "Stage IB" "Stage IIB"
## [36] "Stage IIIA" "Stage II" "Stage IIIA" "Stage IIIB" "Stage IIIB"
## [41] NA "Stage IIIC" "Stage IA" "Stage IB" "Stage IIA"
## [46] "Stage II" "Stage IIB" "Stage II" "Stage IIB" "Stage IA"
## [51] "Stage III" "Stage IIIB" "Stage IV" "Stage IIIC" "Stage IIA"
## [56] "Stage IIIA" "Stage IIB" "Stage IB" NA NA
## [61] "Stage IIA" "Stage IIIB" "Stage IV" NA "Stage IIIB"
## [66] "Stage IIIC" "Stage IIIC" "Stage IV" "Stage II" "Stage II"
## [71] "Stage IIIA" "Stage IV" "Stage IIIC" "Stage IIIB" "Stage IIA"
## [76] "Stage IIB" "Stage IIIA" "Stage IV" "Stage IIA" "Stage IB"
## [81] "Stage IIIA" "Stage IIIA" "Stage IV" "Stage IIIC" NA
## [86] "Stage IIIB" "Stage IV" "Stage IIIA" "Stage IIA" "Stage IB"
## [91] "Stage II" "Stage IIIB" "Stage IIIA" "Stage IIB" "Stage II"
## [96] "Stage IV" "Stage II" "Stage IIIA" "Stage IIIB" "Stage IIIB"
## [101] "Stage IB" "Stage IIB" "Stage IIIB" "Stage IA" "Stage IB"
## [106] "Stage II" "Stage IB" "Stage IIIB" "Stage IB" "Stage IIIA"
## [111] "Stage IB" "Stage IIIC" "Stage IIB" "Stage IIIC" "Stage IV"
## [116] "Stage II" "Stage IIIA" "Stage IIIA" "Stage IIB" "Stage IV"
## [121] "Stage III" NA "Stage IIIB" "Stage IV" "Stage IV"
## [126] "Stage IIA" NA "Stage IIA" "Stage IIA" "Stage IIIA"
## [131] NA "Stage IIIB" "Stage IIB" "Stage IV" "Stage IIB"
## [136] "Stage IIIC" "Stage IB" "Stage IIIC" "Stage IIIB" "Stage IB"
## [141] "Stage IIIB" "Stage IIB" "Stage IIIC" "Stage IIIA" "Stage IA"
## [146] "Stage IIIA" "Stage IIIC" "Stage IIB" "Stage IIB" "Stage IIIB"
## [151] "Stage IA" "Stage IIIB" "Stage IIIA" "Stage IIB" "Stage IV"
## [156] "Stage IIIA" "Stage IV" NA "Stage IV" "Stage IIIB"
## [161] "Stage IIIC" "Stage IIA" "Stage IIIA" "Stage IIIB" "Stage IIIA"
## [166] "Stage IV" "Stage IIB" "Stage IIIC" "Stage IIIB" "Stage IV"
## [171] "Stage IIIA" "Stage IIB" "Stage IIB" "Stage IIIA" "Stage IIB"
## [176] "Stage IIIA" "Stage IIB" "Stage II" "Stage IIIB" "Stage IIIA"
## [181] "Stage IV" "Stage I" "Stage IV" "Stage IIA" "Stage IIIB"
## [186] NA "Stage IIIA" "Stage IB" "Stage IIA" "Stage IB"
## [191] "Stage IIIA" "Stage IIIA" "Stage IIB" "Stage IIIC" "Stage IIA"
## [196] "Stage IA" "Stage IIB" "Stage IIIB" "Stage IIIA" "Stage IIB"
## [201] "Stage IV" "Stage IB" "Stage IV" "Stage IIA" "Stage IIIB"
## [206] "Stage III" "Stage II" "Stage IIIC" "Stage IB" "Stage IIB"
## [211] "Stage IB" "Stage IIIB" "Stage IIIB" "Stage IIA" "Stage IIIA"
## [216] "Stage IIIC" "Stage II" "Stage IV" "Stage IIIC" "Stage IB"
## [221] "Stage IIIA" NA "Stage IB" "Stage IIIB" "Stage IIIA"
## [226] NA "Stage IIIB" "Stage IIB" "Stage IIIB" "Stage IIIC"
## [231] "Stage IV" "Stage IIIA" "Stage IV" "Stage IIA" "Stage IIA"
## [236] "Stage IIIA" "Stage IB" "Stage IIB" "Stage IIIC" "Stage IIIA"
## [241] "Stage II" NA "Stage IIIA" "Stage IIIA" "Stage IIIC"
## [246] "Stage IIA" "Stage IIIB" "Stage IIB" "Stage IV" "Stage IIIC"
## [251] "Stage IIIC" "Stage IIIB" "Stage IIA" "Stage IB" "Stage IB"
## [256] "Stage IIA" "Stage IV" "Stage IV" "Stage IV" NA
## [261] "Stage IIIA" "Stage IIIA" "Stage IA" "Stage IIIA" "Stage IIIC"
## [266] "Stage IV" "Stage IV" "Stage II" "Stage II" "Stage IB"
## [271] "Stage IB" "Stage IA" "Stage IIIB" "Stage IIIA" "Stage IIB"
## [276] "Stage IA" "Stage IIIA" "Stage IB" "Stage IA" "Stage IIIA"
## [281] "Stage IIIA" "Stage IV" "Stage IIB" NA "Stage IIB"
## [286] "Stage IIA" "Stage IIIA" "Stage IIIC" "Stage IV" "Stage IIIC"
## [291] "Stage IIIA" "Stage IIIA" NA "Stage IIIA" "Stage IIIA"
## [296] "Stage IIB" NA "Stage IIB" "Stage IIB" "Stage IIIA"
## [301] "Stage IIIA" "Stage II" "Stage IIA" "Stage IIIA" "Stage IIIA"
## [306] "Stage IIA" "Stage IIA" "Stage IIIA" "Stage IIA" "Stage IIB"
## [311] "Stage IIIB" NA "Stage II" "Stage IIIB" "Stage IV"
## [316] "Stage IIA" "Stage II" "Stage IIIB" "Stage IIIC" "Stage IIB"
## [321] "Stage IIIA" "Stage IIIA" "Stage IIIB" "Stage IIB" "Stage IIIC"
## [326] "Stage IIIB" "Stage II" "Stage IIB" "Stage IIIA" "Stage IB"
## [331] "Stage IIA" "Stage IIA" "Stage II" "Stage IIIB" "Stage IIB"
## [336] "Stage IIB" "Stage IV" "Stage IIB" "Stage IIA" "Stage IIB"
## [341] "Stage IB" "Stage IIB" "Stage IIIB" "Stage IIA" "Stage IIB"
## [346] "Stage IIB" "Stage IV" "Stage IA" "Stage IB" "Stage IIIB"
## [351] "Stage IV" "Stage II" "Stage IIIA" "Stage IIIC" NA
## [356] "Stage IIB" NA "Stage IA" "Stage IIIA" "Stage IIIB"
## [361] "Stage I" "Stage IIIA" "Stage IIIC" "Stage IIA" "Stage IIIA"
## [366] "Stage IIIB" "Stage IIA" "Stage IIB" "Stage IIIA" "Stage IB"
## [371] "Stage IA" "Stage IA" "Stage IIA" "Stage IIIA" "Stage II"
## [376] "Stage IB" "Stage IIIC" "Stage II" "Stage IIIB" "Stage IIB"
## [381] "Stage IB" "Stage IIIB" "Stage IB" "Stage IIIC" "Stage IIIC"
## [386] "Stage IIA" "Stage IB" NA "Stage IIA" "Stage IIIB"
## [391] "Stage IV" "Stage IIB" "Stage IIIA" "Stage IIIB" "Stage IB"
## [396] "Stage IIA" "Stage IB" "Stage IB" "Stage IIA" "Stage IB"
## [401] NA "Stage IIIC" "Stage IIB" "Stage IIIA" "Stage IB"
## [406] "Stage IIIC" "Stage IIIA" "Stage IA" "Stage II" "Stage IIB"
## [411] "Stage IIIA" "Stage IA" "Stage IIIB" "Stage IV" "Stage IIIA"rse$tissue_or_organ_of_origin## [1] "Fundus of stomach" "Body of stomach"
## [3] "Gastric antrum" "Gastric antrum"
## [5] "Gastric antrum" "Body of stomach"
## [7] "Body of stomach" "Body of stomach"
## [9] "Body of stomach" "Cardia, NOS"
## [11] "Gastric antrum" "Gastric antrum"
## [13] "Gastric antrum" "Gastric antrum"
## [15] "Body of stomach" "Gastric antrum"
## [17] "Gastric antrum" "Body of stomach"
## [19] "Body of stomach" "Body of stomach"
## [21] "Fundus of stomach" "Gastric antrum"
## [23] "Gastric antrum" "Fundus of stomach"
## [25] "Stomach, NOS" "Body of stomach"
## [27] "Body of stomach" "Gastric antrum"
## [29] "Body of stomach" "Gastric antrum"
## [31] "Stomach, NOS" "Cardia, NOS"
## [33] "Fundus of stomach" "Fundus of stomach"
## [35] "Body of stomach" "Cardia, NOS"
## [37] "Gastric antrum" "Cardia, NOS"
## [39] "Cardia, NOS" "Fundus of stomach"
## [41] "Cardia, NOS" "Fundus of stomach"
## [43] "Body of stomach" "Fundus of stomach"
## [45] "Cardia, NOS" "Gastric antrum"
## [47] "Gastric antrum" "Cardia, NOS"
## [49] "Body of stomach" "Cardia, NOS"
## [51] "Fundus of stomach" "Gastric antrum"
## [53] "Cardia, NOS" "Gastric antrum"
## [55] "Cardia, NOS" "Body of stomach"
## [57] "Cardia, NOS" "Gastric antrum"
## [59] "Body of stomach" "Gastric antrum"
## [61] "Stomach, NOS" "Cardia, NOS"
## [63] "Gastric antrum" "Gastric antrum"
## [65] "Cardia, NOS" "Fundus of stomach"
## [67] "Fundus of stomach" "Gastric antrum"
## [69] "Gastric antrum" "Cardia, NOS"
## [71] "Gastric antrum" "Gastric antrum"
## [73] "Body of stomach" "Cardia, NOS"
## [75] "Cardia, NOS" "Gastric antrum"
## [77] "Body of stomach" "Cardia, NOS"
## [79] "Cardia, NOS" "Fundus of stomach"
## [81] "Fundus of stomach" "Fundus of stomach"
## [83] "Body of stomach" "Gastric antrum"
## [85] "Body of stomach" "Gastric antrum"
## [87] "Gastric antrum" "Cardia, NOS"
## [89] "Gastric antrum" "Gastric antrum"
## [91] "Gastric antrum" "Gastric antrum"
## [93] "Body of stomach" "Body of stomach"
## [95] "Gastric antrum" "Cardia, NOS"
## [97] "Body of stomach" "Body of stomach"
## [99] "Gastric antrum" "Body of stomach"
## [101] "Cardia, NOS" "Gastric antrum"
## [103] "Cardia, NOS" "Gastric antrum"
## [105] "Fundus of stomach" "Cardia, NOS"
## [107] "Gastric antrum" "Gastric antrum"
## [109] "Body of stomach" "Fundus of stomach"
## [111] "Body of stomach" "Body of stomach"
## [113] "Gastric antrum" "Body of stomach"
## [115] "Cardia, NOS" "Gastric antrum"
## [117] "Body of stomach" "Body of stomach"
## [119] "Cardia, NOS" "Gastric antrum"
## [121] "Stomach, NOS" "Body of stomach"
## [123] "Gastric antrum" "Gastric antrum"
## [125] "Body of stomach" "Body of stomach"
## [127] "Body of stomach" "Body of stomach"
## [129] "Body of stomach" "Stomach, NOS"
## [131] "Stomach, NOS" "Gastric antrum"
## [133] "Gastric antrum" "Stomach, NOS"
## [135] "Fundus of stomach" "Body of stomach"
## [137] "Stomach, NOS" "Body of stomach"
## [139] "Body of stomach" "Fundus of stomach"
## [141] "Gastric antrum" "Gastric antrum"
## [143] "Gastric antrum" "Gastric antrum"
## [145] "Gastric antrum" "Cardia, NOS"
## [147] "Body of stomach" "Body of stomach"
## [149] "Body of stomach" "Gastric antrum"
## [151] "Cardia, NOS" "Cardia, NOS"
## [153] "Body of stomach" "Cardia, NOS"
## [155] "Gastric antrum" "Cardia, NOS"
## [157] "Body of stomach" "Cardia, NOS"
## [159] "Cardia, NOS" "Cardia, NOS"
## [161] "Gastric antrum" "Gastric antrum"
## [163] "Gastric antrum" "Body of stomach"
## [165] "Gastric antrum" "Body of stomach"
## [167] "Fundus of stomach" "Gastric antrum"
## [169] "Cardia, NOS" "Stomach, NOS"
## [171] "Cardia, NOS" "Body of stomach"
## [173] "Gastric antrum" "Gastric antrum"
## [175] "Cardia, NOS" "Gastric antrum"
## [177] "Gastric antrum" "Cardia, NOS"
## [179] "Body of stomach" "Gastric antrum"
## [181] "Gastric antrum" "Gastric antrum"
## [183] "Cardia, NOS" "Fundus of stomach"
## [185] "Fundus of stomach" "Body of stomach"
## [187] "Gastric antrum" "Body of stomach"
## [189] "Gastric antrum" "Gastric antrum"
## [191] "Body of stomach" "Gastric antrum"
## [193] "Cardia, NOS" "Fundus of stomach"
## [195] "Cardia, NOS" "Cardia, NOS"
## [197] "Cardia, NOS" "Body of stomach"
## [199] "Gastric antrum" "Gastric antrum"
## [201] "Body of stomach" "Fundus of stomach"
## [203] "Gastric antrum" "Fundus of stomach"
## [205] "Gastric antrum" "Body of stomach"
## [207] "Gastric antrum" "Gastric antrum"
## [209] "Lesser curvature of stomach, NOS" "Body of stomach"
## [211] "Gastric antrum" "Cardia, NOS"
## [213] "Gastric antrum" "Body of stomach"
## [215] "Body of stomach" "Body of stomach"
## [217] "Gastric antrum" "Stomach, NOS"
## [219] "Gastric antrum" "Cardia, NOS"
## [221] "Cardia, NOS" "Stomach, NOS"
## [223] "Cardia, NOS" "Fundus of stomach"
## [225] "Cardia, NOS" "Cardia, NOS"
## [227] "Cardia, NOS" "Fundus of stomach"
## [229] "Cardia, NOS" "Fundus of stomach"
## [231] "Gastric antrum" "Fundus of stomach"
## [233] "Body of stomach" "Fundus of stomach"
## [235] "Body of stomach" "Body of stomach"
## [237] "Cardia, NOS" "Cardia, NOS"
## [239] "Gastric antrum" "Cardia, NOS"
## [241] "Gastric antrum" "Cardia, NOS"
## [243] "Gastric antrum" "Gastric antrum"
## [245] "Fundus of stomach" "Gastric antrum"
## [247] "Body of stomach" "Gastric antrum"
## [249] "Gastric antrum" "Cardia, NOS"
## [251] "Fundus of stomach" "Body of stomach"
## [253] "Fundus of stomach" "Cardia, NOS"
## [255] "Cardia, NOS" "Gastric antrum"
## [257] "Gastric antrum" "Stomach, NOS"
## [259] "Cardia, NOS" "Gastric antrum"
## [261] "Gastric antrum" "Gastric antrum"
## [263] "Body of stomach" "Gastric antrum"
## [265] "Fundus of stomach" "Gastric antrum"
## [267] "Cardia, NOS" "Gastric antrum"
## [269] "Cardia, NOS" "Cardia, NOS"
## [271] "Gastric antrum" "Stomach, NOS"
## [273] "Gastric antrum" "Fundus of stomach"
## [275] "Body of stomach" "Body of stomach"
## [277] "Body of stomach" "Gastric antrum"
## [279] "Body of stomach" "Gastric antrum"
## [281] "Cardia, NOS" "Body of stomach"
## [283] "Gastric antrum" "Pylorus"
## [285] "Fundus of stomach" "Cardia, NOS"
## [287] "Body of stomach" "Gastric antrum"
## [289] "Gastric antrum" "Gastric antrum"
## [291] "Gastric antrum" "Cardia, NOS"
## [293] "Cardia, NOS" "Cardia, NOS"
## [295] "Gastric antrum" "Body of stomach"
## [297] "Body of stomach" "Cardia, NOS"
## [299] "Gastric antrum" "Gastric antrum"
## [301] "Cardia, NOS" "Gastric antrum"
## [303] "Cardia, NOS" "Gastric antrum"
## [305] "Body of stomach" "Stomach, NOS"
## [307] "Cardia, NOS" "Gastric antrum"
## [309] "Body of stomach" "Gastric antrum"
## [311] "Gastric antrum" "Gastric antrum"
## [313] "Gastric antrum" "Gastric antrum"
## [315] "Body of stomach" "Body of stomach"
## [317] "Body of stomach" "Gastric antrum"
## [319] "Cardia, NOS" "Fundus of stomach"
## [321] "Body of stomach" "Gastric antrum"
## [323] "Gastric antrum" "Gastric antrum"
## [325] "Gastric antrum" "Gastric antrum"
## [327] "Cardia, NOS" "Body of stomach"
## [329] "Gastric antrum" "Cardia, NOS"
## [331] "Gastric antrum" "Gastric antrum"
## [333] "Stomach, NOS" "Body of stomach"
## [335] "Gastric antrum" "Cardia, NOS"
## [337] "Fundus of stomach" "Body of stomach"
## [339] "Body of stomach" "Gastric antrum"
## [341] "Gastric antrum" "Gastric antrum"
## [343] "Fundus of stomach" "Cardia, NOS"
## [345] "Fundus of stomach" "Cardia, NOS"
## [347] "Gastric antrum" "Body of stomach"
## [349] "Cardia, NOS" "Cardia, NOS"
## [351] "Gastric antrum" "Gastric antrum"
## [353] "Fundus of stomach" "Body of stomach"
## [355] "Gastric antrum" "Gastric antrum"
## [357] "Cardia, NOS" "Cardia, NOS"
## [359] "Cardia, NOS" "Gastric antrum"
## [361] "Cardia, NOS" "Cardia, NOS"
## [363] "Cardia, NOS" "Gastric antrum"
## [365] "Cardia, NOS" "Cardia, NOS"
## [367] "Gastric antrum" "Fundus of stomach"
## [369] "Body of stomach" "Cardia, NOS"
## [371] "Body of stomach" "Cardia, NOS"
## [373] "Cardia, NOS" "Fundus of stomach"
## [375] "Gastric antrum" "Body of stomach"
## [377] "Fundus of stomach" "Fundus of stomach"
## [379] "Stomach, NOS" "Gastric antrum"
## [381] "Fundus of stomach" "Gastric antrum"
## [383] "Stomach, NOS" "Gastric antrum"
## [385] "Cardia, NOS" "Gastric antrum"
## [387] "Body of stomach" "Cardia, NOS"
## [389] "Gastric antrum" "Cardia, NOS"
## [391] "Cardia, NOS" "Gastric antrum"
## [393] "Body of stomach" "Body of stomach"
## [395] "Gastric antrum" "Stomach, NOS"
## [397] "Gastric antrum" "Body of stomach"
## [399] "Body of stomach" "Fundus of stomach"
## [401] "Gastric antrum" "Body of stomach"
## [403] "Body of stomach" "Body of stomach"
## [405] "Cardia, NOS" "Gastric antrum"
## [407] "Gastric antrum" "Body of stomach"
## [409] "Cardia, NOS" "Gastric antrum"
## [411] "Gastric antrum" "Fundus of stomach"
## [413] "Cardia, NOS" "Cardia, NOS"
## [415] "Fundus of stomach"rse$days_to_last_follow_up## [1] 378 21 170 725 1133 30 882 399 NA 411 18 600 229 580 1072
## [16] 0 352 900 0 1200 NA 408 46 1236 0 899 356 NA 1000 NA
## [31] 699 402 NA 0 19 582 543 1010 77 500 NA 11 23 NA 378
## [46] 1023 392 2496 344 383 25 427 666 21 1367 820 5 579 0 NA
## [61] 131 11 972 0 NA 65 0 365 485 126 176 NA 0 325 104
## [76] 989 385 198 20 NA 7 383 NA 113 NA 16 NA 17 694 428
## [91] 895 647 881 942 400 1674 12 940 411 564 440 268 356 NA 476
## [106] 3 566 35 NA 288 0 64 431 NA 21 2 523 NA 1106 92
## [121] 0 0 NA 262 21 485 0 1055 NA 0 0 35 342 1918 628
## [136] 225 243 7 641 724 419 237 856 8 NA NA 678 1210 981 212
## [151] 479 NA 376 413 374 376 NA 0 92 NA NA 415 344 3519 375
## [166] NA 511 NA 411 2267 1297 812 1190 1862 29 NA 679 1124 NA 644
## [181] 0 0 1389 337 825 564 2171 1935 371 NA NA 521 572 946 519
## [196] 738 40 NA NA 180 8 754 NA 90 477 NA 280 NA 1765 1145
## [211] NA 422 664 949 NA NA 367 NA 650 613 NA 0 NA 6 156
## [226] 625 838 335 NA 28 183 22 NA 593 416 1132 NA NA NA 47
## [241] 388 0 NA 3 951 912 3720 496 0 1184 280 1319 29 942 12
## [256] 34 1645 NA NA 0 1016 15 1100 NA 675 NA 1138 2 1083 678
## [271] 3540 1964 NA 381 47 1588 0 NA 742 1690 NA NA 819 0 287
## [286] NA 1160 928 NA 22 383 864 158 NA 838 574 0 1646 692 NA
## [301] 181 NA 2 523 NA 346 594 20 997 636 813 0 468 494 31
## [316] 1023 31 1153 19 389 1431 573 NA 991 482 24 245 213 164 2032
## [331] 14 NA 0 421 4 594 NA 308 1223 690 643 739 418 0 1108
## [346] 323 0 736 NA NA NA 396 618 15 0 200 NA 379 607 394
## [361] 559 434 NA 4 NA 38 785 224 1851 621 358 NA 1038 450 2351
## [376] 1090 595 377 NA NA 131 99 NA 616 1328 198 463 189 273 1002
## [391] NA 449 25 1484 525 427 0 375 491 384 0 45 486 389 577
## [406] 92 NA 912 NA 374 862 0 752 NA 390rse$primary_diagnosis## [1] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [3] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [5] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [7] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [9] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [11] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [13] "Adenocarcinoma, intestinal type" "Mucinous adenocarcinoma"
## [15] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [17] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [19] "Adenocarcinoma, NOS" "Mucinous adenocarcinoma"
## [21] "Carcinoma, diffuse type" "Mucinous adenocarcinoma"
## [23] "Tubular adenocarcinoma" "Carcinoma, diffuse type"
## [25] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [27] "Carcinoma, diffuse type" "Carcinoma, diffuse type"
## [29] "Tubular adenocarcinoma" "Adenocarcinoma, intestinal type"
## [31] "Adenocarcinoma with mixed subtypes" "Adenocarcinoma, NOS"
## [33] "Mucinous adenocarcinoma" "Adenocarcinoma, NOS"
## [35] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [37] "Carcinoma, diffuse type" "Mucinous adenocarcinoma"
## [39] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [41] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [43] "Tubular adenocarcinoma" "Carcinoma, diffuse type"
## [45] "Adenocarcinoma, NOS" "Papillary adenocarcinoma, NOS"
## [47] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [49] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [51] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [53] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [55] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [57] "Adenocarcinoma, NOS" "Signet ring cell carcinoma"
## [59] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [61] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [63] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [65] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [67] "Adenocarcinoma, NOS" "Adenocarcinoma with mixed subtypes"
## [69] "Adenocarcinoma, NOS" "Papillary adenocarcinoma, NOS"
## [71] "Mucinous adenocarcinoma" "Carcinoma, diffuse type"
## [73] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [75] "Adenocarcinoma, NOS" "Mucinous adenocarcinoma"
## [77] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [79] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [81] "Tubular adenocarcinoma" "Carcinoma, diffuse type"
## [83] "Papillary adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [85] "Signet ring cell carcinoma" "Adenocarcinoma, NOS"
## [87] "Tubular adenocarcinoma" "Adenocarcinoma, intestinal type"
## [89] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [91] "Adenocarcinoma, NOS" "Mucinous adenocarcinoma"
## [93] "Tubular adenocarcinoma" "Adenocarcinoma, intestinal type"
## [95] "Papillary adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [97] "Mucinous adenocarcinoma" "Adenocarcinoma, NOS"
## [99] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [101] "Adenocarcinoma, intestinal type" "Carcinoma, diffuse type"
## [103] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [105] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [107] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [109] "Signet ring cell carcinoma" "Adenocarcinoma, intestinal type"
## [111] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [113] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [115] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [117] "Tubular adenocarcinoma" "Adenocarcinoma, intestinal type"
## [119] "Carcinoma, diffuse type" "Signet ring cell carcinoma"
## [121] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [123] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [125] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [127] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [129] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [131] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [133] "Adenocarcinoma, NOS" "Mucinous adenocarcinoma"
## [135] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [137] "Adenocarcinoma, intestinal type" "Signet ring cell carcinoma"
## [139] "Carcinoma, diffuse type" "Papillary adenocarcinoma, NOS"
## [141] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [143] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [145] "Adenocarcinoma, intestinal type" "Carcinoma, diffuse type"
## [147] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [149] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [151] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [153] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [155] "Mucinous adenocarcinoma" "Tubular adenocarcinoma"
## [157] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [159] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [161] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [163] "Tubular adenocarcinoma" "Carcinoma, diffuse type"
## [165] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [167] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [169] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [171] "Tubular adenocarcinoma" "Carcinoma, diffuse type"
## [173] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [175] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [177] "Carcinoma, diffuse type" "Carcinoma, diffuse type"
## [179] "Carcinoma, diffuse type" "Tubular adenocarcinoma"
## [181] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [183] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [185] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [187] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [189] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [191] "Adenocarcinoma, intestinal type" "Tubular adenocarcinoma"
## [193] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [195] "Adenocarcinoma, NOS" "Papillary adenocarcinoma, NOS"
## [197] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [199] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [201] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [203] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [205] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [207] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [209] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [211] "Carcinoma, diffuse type" "Tubular adenocarcinoma"
## [213] "Adenocarcinoma, intestinal type" "Carcinoma, diffuse type"
## [215] "Adenocarcinoma, intestinal type" "Tubular adenocarcinoma"
## [217] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [219] "Carcinoma, diffuse type" "Signet ring cell carcinoma"
## [221] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [223] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [225] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [227] "Adenocarcinoma, intestinal type" "Adenocarcinoma, intestinal type"
## [229] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [231] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [233] "Adenocarcinoma, intestinal type" "Tubular adenocarcinoma"
## [235] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [237] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [239] "Tubular adenocarcinoma" "Signet ring cell carcinoma"
## [241] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [243] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [245] "Adenocarcinoma, intestinal type" "Tubular adenocarcinoma"
## [247] "Adenocarcinoma, intestinal type" "Carcinoma, diffuse type"
## [249] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [251] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [253] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [255] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [257] "Adenocarcinoma, intestinal type" "Carcinoma, diffuse type"
## [259] "Signet ring cell carcinoma" "Adenocarcinoma, NOS"
## [261] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [263] "Papillary adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [265] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [267] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [269] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [271] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [273] "Adenocarcinoma, intestinal type" "Adenocarcinoma, intestinal type"
## [275] "Adenocarcinoma, intestinal type" "Adenocarcinoma, intestinal type"
## [277] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [279] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [281] "Tubular adenocarcinoma" "Adenocarcinoma, intestinal type"
## [283] "Signet ring cell carcinoma" "Adenocarcinoma, NOS"
## [285] "Adenocarcinoma, intestinal type" "Adenocarcinoma, intestinal type"
## [287] "Mucinous adenocarcinoma" "Mucinous adenocarcinoma"
## [289] "Signet ring cell carcinoma" "Adenocarcinoma, intestinal type"
## [291] "Mucinous adenocarcinoma" "Adenocarcinoma, NOS"
## [293] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [295] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [297] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [299] "Tubular adenocarcinoma" "Signet ring cell carcinoma"
## [301] "Carcinoma, diffuse type" "Tubular adenocarcinoma"
## [303] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [305] "Tubular adenocarcinoma" "Adenocarcinoma, intestinal type"
## [307] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [309] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [311] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [313] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [315] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [317] "Adenocarcinoma, intestinal type" "Adenocarcinoma, intestinal type"
## [319] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [321] "Carcinoma, diffuse type" "Tubular adenocarcinoma"
## [323] "Tubular adenocarcinoma" "Mucinous adenocarcinoma"
## [325] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [327] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [329] "Adenocarcinoma, intestinal type" "Tubular adenocarcinoma"
## [331] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [333] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [335] "Adenocarcinoma, NOS" "Mucinous adenocarcinoma"
## [337] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [339] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [341] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [343] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [345] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [347] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [349] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [351] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [353] "Adenocarcinoma, intestinal type" "Mucinous adenocarcinoma"
## [355] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [357] "Carcinoma, diffuse type" "Adenocarcinoma, NOS"
## [359] "Adenocarcinoma, intestinal type" "Tubular adenocarcinoma"
## [361] "Adenocarcinoma, NOS" "Tubular adenocarcinoma"
## [363] "Signet ring cell carcinoma" "Carcinoma, diffuse type"
## [365] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [367] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [369] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [371] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [373] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [375] "Mucinous adenocarcinoma" "Adenocarcinoma, NOS"
## [377] "Carcinoma, diffuse type" "Carcinoma, diffuse type"
## [379] "Adenocarcinoma, NOS" "Signet ring cell carcinoma"
## [381] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [383] "Adenocarcinoma, NOS" "Carcinoma, diffuse type"
## [385] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [387] "Tubular adenocarcinoma" "Adenocarcinoma, NOS"
## [389] "Carcinoma, diffuse type" "Adenocarcinoma, intestinal type"
## [391] "Tubular adenocarcinoma" "Mucinous adenocarcinoma"
## [393] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [395] "Adenocarcinoma, intestinal type" "Adenocarcinoma, NOS"
## [397] "Adenocarcinoma, intestinal type" "Tubular adenocarcinoma"
## [399] "Adenocarcinoma, NOS" "Adenocarcinoma, NOS"
## [401] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [403] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [405] "Adenocarcinoma, intestinal type" "Carcinoma, diffuse type"
## [407] "Adenocarcinoma, NOS" "Adenocarcinoma, intestinal type"
## [409] "Adenocarcinoma, intestinal type" "Carcinoma, diffuse type"
## [411] "Mucinous adenocarcinoma" "Adenocarcinoma, NOS"
## [413] "Tubular adenocarcinoma" "Tubular adenocarcinoma"
## [415] "Adenocarcinoma, NOS"rse$ajcc_pathologic_t## [1] "T3" "T4b" "T2" "T2" "T4a" "T3" "T4a" "T3" "T4b" "T3" "T4a" "T3"
## [13] "T3" "T2" "T3" "TX" "T3" "T4a" "T2" "T3" "T4a" "T3" "T3" "T3"
## [25] "T4" "T4b" "T2" "T3" "T4b" "T2" "T3" "T3" "T3" "T2" "T4a" "T2"
## [37] "T2" "T4a" "T3" "T3" "T3" "T4b" "T1b" "T2" "T3" "T3" "T4a" "T2"
## [49] "T2" "T1b" "T4" "T3" "T3" "T4a" "T3" "T4a" "T3" "T2" "T1" "T4a"
## [61] "T3" "T3" "T4b" "TX" "T3" "T4b" "T4b" "T4" "T2a" "T2" "T3" "T4"
## [73] "T4b" "T3" "T3" "T4a" "T3" "T3" "T3" "T2" "T3" "T3" "T3" "T4b"
## [85] "T4" "T4a" "T4" "T3" "T3" "T1b" "T3" "T3" "T3" "T4a" "T3" "T2"
## [97] "T3" "T3" "T4a" "T3" "T2" "T2" "T3" "T2" "T2" "T3" "T2" "T4a"
## [109] "T2b" "T4" "T2a" "T4a" "T4a" "T4a" "T4" "T2" "T3" "T2" "T3" "T4a"
## [121] "T2b" "T3" "T3" "T4" "T3" "T2" "T3" "T3" "T3" "T3" "TX" "T3"
## [133] "T2" "T2b" "T4a" "T4b" "T2" "T4b" "T4a" "T2" "T3" "T3" "T4a" "T4"
## [145] "T1" "T3" "T4a" "T3" "T4a" "T3" "T1b" "T3" "T2" "T3" "T4" "T2"
## [157] "T4" "T2a" "T4" "T3" "T4a" "T3" "T3" "T3" "T4" "T4" "T2" "T4a"
## [169] "T3" "T4" "T3" "T4a" "T3" "T3" "T3" "T3" "T4a" "T2b" "T3" "T3"
## [181] "T4a" "T1b" "T3" "T3" "T4b" "T2b" "T3" "T1" "T3" "T2" "T3" "T4a"
## [193] "T2" "T4b" "T3" "T1b" "T2" "T3" "T3" "T3" "T4" "T2" "T4a" "T3"
## [205] "T4b" "T3" "T3" "T4a" "T2b" "T3" "T2a" "T3" "T4b" "T3" "T3" "T4a"
## [217] "T3" "T3" "T4" "T2" "T3" "TX" "T2" "T4b" "T3" "T2" "T4a" "T4a"
## [229] "T3" "T4b" "T4" "T4a" "T4" "T3" "T3" "T4" "T2a" "T2" "T4b" "T3"
## [241] "T3" "TX" "T3" "T3" "T4b" "T2" "T3" "T3" "T4a" "T4" "T4" "T3"
## [253] "T3" "T2a" "T2" "T3" "T4" "T3" "T4" "TX" "T3" "T3" "T1b" "T3"
## [265] "T4b" "T3" "T3" "T3" "T2" "T2" "T2" "T1" "T3" "T3" "T4a" "T1"
## [277] "T3" "T2" "T1a" "T3" "T3" "T3" "T4a" "T3" "T4a" "T3" "T4a" "T4a"
## [289] "T4" "T4a" "T3" "T3" "T2" "T3" "T4a" "T4a" "T2a" "T3" "T3" "T3"
## [301] "T2" "T3" "T3" "T2" "T3" "T3" "T1b" "T4a" "T3" "T2" "T3" "TX"
## [313] "T3" "T4b" "T4" "T3" "T2b" "T3" "T4b" "T4a" "T2b" "T2b" "T3" "T4a"
## [325] "T4b" "T4a" "T2" "T3" "T3" "T2b" "T3" "T3" "T2a" "T3" "T3" "T3"
## [337] "T3" "T3" "T3" "T3" "T2" "T3" "T3" "T3" "T3" "T3" "T4" "T1a"
## [349] "T2" "T3" "T3" "T2" "T3" "T4" "TX" "T3" "T3" "T1b" "T3" "T3"
## [361] "T1b" "T2" "T4a" "T3" "T3" "T3" "T3" "T3" "T3" "T2" "T1b" "T1b"
## [373] "T3" "T4a" "T2b" "T2" "T4" "T3" "T3" "T4a" "T2" "T4a" "T2b" "T4b"
## [385] "T4a" "T3" "T2" "T1b" "T2" "T3" "T3" "T2" "T3" "T3" "T2" "T2"
## [397] "T2" "T2" "T3" "T2" "TX" "T4b" "T2" "T2b" "T2a" "T4a" "T4a" "T1"
## [409] "T2b" "T3" "T4a" "T1b" "T3" "T4" "T3"rse$ajcc_pathologic_n## [1] "N0" "N1" "N2" "N2" "N2" "N2" "N3b" "N1" "N2" "N0" "N2" "N2"
## [13] "N3a" "N1" "N0" "N1" "N3a" "N0" "NX" "N3a" "N3" "N0" NA "N2"
## [25] "N0" "N0" "N0" "N1" "N1" "N2" "N1" "N1" "N1" "N0" "N0" "N3"
## [37] "N1" "N1" "N2" "N3a" "N1" "N3a" "N0" "N0" "N0" "N0" "N0" "N1"
## [49] "N1" "N0" "N1" "N3a" "N3a" "N3a" "N0" "N1" "N1" "N0" "NX" "N2"
## [61] "N0" "N3a" "N2" "NX" "N3" "N2" "N3a" "N1" "N1" "N1" "N2" "N3"
## [73] "N3a" "N3a" "N0" "NX" "N2" "N3" "N0" "N0" "N2" "N1" "N3" "N2"
## [85] "NX" "N2" "N3" "N2" "N0" "N1" "N0" "N3b" "N2" "N0" "N0" "N3"
## [97] "N0" "N2" "N2" "N3a" "N0" "N2" "N3" "N0" "N0" "N0" "N0" "N2"
## [109] "N0" NA "N0" "N3b" "N0" "N3" "N1" "N1" "N2" "N2" "N1" "N3a"
## [121] "N1" "NX" "N3" "N1" "N3a" "N1" "NX" "N0" "N0" "N1" "N1" "N3a"
## [133] "N2" "N3" "N0" "N3a" "N0" "N3a" "N2" "N0" "N3a" "N1" "N3a" "N1"
## [145] "N0" "N1" "N3a" "N1" "N0" "N3a" "N0" "N2" "N3" "N1" "N0" "N3"
## [157] "N1" "NX" "N1" "N3a" "N3b" "N0" "N2" "N2" "N0" "N2" "N2" "N3"
## [169] "N3a" "N1" "N2" "N0" "N1" "N1" "N1" "N1" "N0" "N1" "N3" "N2"
## [181] "N2" "N1" "N1" "N0" "N1" "N2" "N1" "N1" "N0" "N0" "N2" "N1"
## [193] "N1" "N2" "N0" "N0" "N2" "N3b" "N2" "N1" "N3a" "N0" "N1" "N0"
## [205] "N1" "NX" "N0" "N3" "N0" "N1" "N0" "N3a" "N0" "N0" "N1" "N3b"
## [217] "N0" "N3" "N3a" "N0" "N1" "N1" "N0" "N1" "N2" "N1" "N2" "NX"
## [229] "N2" "N3a" "N1" "N1" "N1" "N0" "N0" "N1" "N0" "N2" "N2" "N2"
## [241] "N0" "NX" "N2" "N1" "N3a" "N1" "N2" "N1" "N2" "N3a" "N3a" "N2"
## [253] "N0" "N0" "N0" "N0" "N2" "N3" "N3" "NX" "N2" "N1" "N0" "N1"
## [265] "N2" "N2" "N1" "N0" "N1" "N0" "N0" "N0" "N2" "N1" "N0" "N0"
## [277] "N1" "N0" "N0" "N1" "N2" "N3" "N0" "N1" "NX" "N0" "N1" "N3a"
## [289] "N3" "N3a" "N1" "N2" "N1" "N1" "N1" "N0" "NX" "N1" "N1" "N1"
## [301] "N2" "N0" "N0" "N3a" "N1" "N0" "N2" "N1" "N0" "N2" "N3a" "NX"
## [313] "N0" "N1" "N0" "N0" "N1" "N2" "N2" "N0" "N2" "N2" "N3a" "N0"
## [325] "N3a" "N2" "N1" "N1" "N2" "N0" "N0" "N0" "N1" "N3a" "N1" "N1"
## [337] "N3" "N1" "N0" "N1" "N0" "N1" "N3a" "N0" "N1" "N1" "N2" "N0"
## [349] "N0" "N2" "N3" "N1" "N2" "N3a" "NX" "N1" "N3" "N0" "N2" "N3b"
## [361] "N0" "N3a" "N3a" "N0" "N1" "N3a" "N0" "N1" "N1" "N0" "N0" "N0"
## [373] "N0" "N1" "N1" "N0" "N3" "N0" "N2" "N0" "N0" "N2" "N0" "N2"
## [385] "N3" "N0" "N0" "N1" "N1" "N2" "N3" "N2" "N2" "N3a" "N0" "NX"
## [397] "N0" "N0" "N0" "N0" "N1" "N2" "N2" "N3" "N0" "N3a" "N1" "N0"
## [409] "N1" "N1" "N1" "N0" "N3a" "N1" "N1"rse$ajcc_pathologic_m## [1] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [16] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [31] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0"
## [46] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [61] "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0"
## [76] "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "MX" "M0" "M0" "MX" "M0" "M0"
## [91] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [106] "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1"
## [121] "M0" "MX" "M0" "M0" "M1" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [136] "M0" "M0" "MX" "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "MX" "M0" "M0" "M0"
## [151] "M0" "M0" "M0" "MX" "M1" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0"
## [166] "M1" "M0" "MX" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [181] "M1" "MX" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "MX"
## [196] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "MX" "M0"
## [211] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [226] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [241] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "MX"
## [256] "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M1" "M0" "M0" "M0"
## [271] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0"
## [286] "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [301] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "MX" "M1"
## [316] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [331] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [346] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0"
## [361] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [376] "M0" "M0" "M0" "MX" "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [391] "M0" "M0" "M0" "M0" "MX" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [406] "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0"rse$site_of_resection_or_biopsy## [1] "Fundus of stomach" "Body of stomach"
## [3] "Gastric antrum" "Gastric antrum"
## [5] "Gastric antrum" "Body of stomach"
## [7] "Body of stomach" "Body of stomach"
## [9] "Body of stomach" "Cardia, NOS"
## [11] "Gastric antrum" "Gastric antrum"
## [13] "Gastric antrum" "Gastric antrum"
## [15] "Body of stomach" "Gastric antrum"
## [17] "Gastric antrum" "Body of stomach"
## [19] "Body of stomach" "Body of stomach"
## [21] "Fundus of stomach" "Gastric antrum"
## [23] "Gastric antrum" "Fundus of stomach"
## [25] "Stomach, NOS" "Body of stomach"
## [27] "Body of stomach" "Gastric antrum"
## [29] "Body of stomach" "Gastric antrum"
## [31] "Stomach, NOS" "Cardia, NOS"
## [33] "Fundus of stomach" "Fundus of stomach"
## [35] "Body of stomach" "Cardia, NOS"
## [37] "Gastric antrum" "Cardia, NOS"
## [39] "Cardia, NOS" "Fundus of stomach"
## [41] "Cardia, NOS" "Fundus of stomach"
## [43] "Body of stomach" "Fundus of stomach"
## [45] "Cardia, NOS" "Gastric antrum"
## [47] "Gastric antrum" "Cardia, NOS"
## [49] "Body of stomach" "Cardia, NOS"
## [51] "Fundus of stomach" "Gastric antrum"
## [53] "Cardia, NOS" "Gastric antrum"
## [55] "Cardia, NOS" "Body of stomach"
## [57] "Cardia, NOS" "Gastric antrum"
## [59] "Body of stomach" "Gastric antrum"
## [61] "Stomach, NOS" "Cardia, NOS"
## [63] "Gastric antrum" "Gastric antrum"
## [65] "Cardia, NOS" "Fundus of stomach"
## [67] "Fundus of stomach" "Gastric antrum"
## [69] "Gastric antrum" "Cardia, NOS"
## [71] "Gastric antrum" "Gastric antrum"
## [73] "Body of stomach" "Cardia, NOS"
## [75] "Cardia, NOS" "Gastric antrum"
## [77] "Body of stomach" "Cardia, NOS"
## [79] "Cardia, NOS" "Fundus of stomach"
## [81] "Fundus of stomach" "Fundus of stomach"
## [83] "Body of stomach" "Gastric antrum"
## [85] "Body of stomach" "Gastric antrum"
## [87] "Gastric antrum" "Cardia, NOS"
## [89] "Gastric antrum" "Gastric antrum"
## [91] "Gastric antrum" "Gastric antrum"
## [93] "Body of stomach" "Body of stomach"
## [95] "Gastric antrum" "Cardia, NOS"
## [97] "Body of stomach" "Body of stomach"
## [99] "Gastric antrum" "Body of stomach"
## [101] "Cardia, NOS" "Gastric antrum"
## [103] "Cardia, NOS" "Gastric antrum"
## [105] "Fundus of stomach" "Cardia, NOS"
## [107] "Gastric antrum" "Gastric antrum"
## [109] "Body of stomach" "Fundus of stomach"
## [111] "Body of stomach" "Body of stomach"
## [113] "Gastric antrum" "Body of stomach"
## [115] "Cardia, NOS" "Gastric antrum"
## [117] "Body of stomach" "Body of stomach"
## [119] "Cardia, NOS" "Gastric antrum"
## [121] "Stomach, NOS" "Body of stomach"
## [123] "Gastric antrum" "Gastric antrum"
## [125] "Body of stomach" "Body of stomach"
## [127] "Body of stomach" "Body of stomach"
## [129] "Body of stomach" "Stomach, NOS"
## [131] "Stomach, NOS" "Gastric antrum"
## [133] "Gastric antrum" "Stomach, NOS"
## [135] "Fundus of stomach" "Body of stomach"
## [137] "Stomach, NOS" "Body of stomach"
## [139] "Body of stomach" "Fundus of stomach"
## [141] "Gastric antrum" "Gastric antrum"
## [143] "Gastric antrum" "Gastric antrum"
## [145] "Gastric antrum" "Cardia, NOS"
## [147] "Body of stomach" "Body of stomach"
## [149] "Body of stomach" "Gastric antrum"
## [151] "Cardia, NOS" "Cardia, NOS"
## [153] "Body of stomach" "Cardia, NOS"
## [155] "Gastric antrum" "Cardia, NOS"
## [157] "Body of stomach" "Cardia, NOS"
## [159] "Cardia, NOS" "Cardia, NOS"
## [161] "Gastric antrum" "Gastric antrum"
## [163] "Gastric antrum" "Body of stomach"
## [165] "Gastric antrum" "Body of stomach"
## [167] "Fundus of stomach" "Gastric antrum"
## [169] "Cardia, NOS" "Stomach, NOS"
## [171] "Cardia, NOS" "Body of stomach"
## [173] "Gastric antrum" "Gastric antrum"
## [175] "Cardia, NOS" "Gastric antrum"
## [177] "Gastric antrum" "Cardia, NOS"
## [179] "Body of stomach" "Gastric antrum"
## [181] "Gastric antrum" "Gastric antrum"
## [183] "Cardia, NOS" "Fundus of stomach"
## [185] "Fundus of stomach" "Body of stomach"
## [187] "Gastric antrum" "Body of stomach"
## [189] "Gastric antrum" "Gastric antrum"
## [191] "Body of stomach" "Gastric antrum"
## [193] "Cardia, NOS" "Fundus of stomach"
## [195] "Cardia, NOS" "Cardia, NOS"
## [197] "Cardia, NOS" "Body of stomach"
## [199] "Gastric antrum" "Gastric antrum"
## [201] "Body of stomach" "Fundus of stomach"
## [203] "Gastric antrum" "Fundus of stomach"
## [205] "Gastric antrum" "Body of stomach"
## [207] "Gastric antrum" "Gastric antrum"
## [209] "Lesser curvature of stomach, NOS" "Body of stomach"
## [211] "Gastric antrum" "Cardia, NOS"
## [213] "Gastric antrum" "Body of stomach"
## [215] "Body of stomach" "Body of stomach"
## [217] "Gastric antrum" "Stomach, NOS"
## [219] "Gastric antrum" "Cardia, NOS"
## [221] "Cardia, NOS" "Stomach, NOS"
## [223] "Cardia, NOS" "Fundus of stomach"
## [225] "Cardia, NOS" "Cardia, NOS"
## [227] "Cardia, NOS" "Fundus of stomach"
## [229] "Cardia, NOS" "Fundus of stomach"
## [231] "Gastric antrum" "Fundus of stomach"
## [233] "Body of stomach" "Fundus of stomach"
## [235] "Body of stomach" "Body of stomach"
## [237] "Cardia, NOS" "Cardia, NOS"
## [239] "Gastric antrum" "Cardia, NOS"
## [241] "Gastric antrum" "Cardia, NOS"
## [243] "Gastric antrum" "Gastric antrum"
## [245] "Fundus of stomach" "Gastric antrum"
## [247] "Body of stomach" "Gastric antrum"
## [249] "Gastric antrum" "Cardia, NOS"
## [251] "Fundus of stomach" "Body of stomach"
## [253] "Fundus of stomach" "Cardia, NOS"
## [255] "Cardia, NOS" "Gastric antrum"
## [257] "Gastric antrum" "Stomach, NOS"
## [259] "Cardia, NOS" "Gastric antrum"
## [261] "Gastric antrum" "Gastric antrum"
## [263] "Body of stomach" "Gastric antrum"
## [265] "Fundus of stomach" "Gastric antrum"
## [267] "Cardia, NOS" "Gastric antrum"
## [269] "Cardia, NOS" "Cardia, NOS"
## [271] "Gastric antrum" "Stomach, NOS"
## [273] "Gastric antrum" "Fundus of stomach"
## [275] "Body of stomach" "Body of stomach"
## [277] "Body of stomach" "Gastric antrum"
## [279] "Body of stomach" "Gastric antrum"
## [281] "Cardia, NOS" "Body of stomach"
## [283] "Gastric antrum" "Pylorus"
## [285] "Fundus of stomach" "Cardia, NOS"
## [287] "Body of stomach" "Gastric antrum"
## [289] "Gastric antrum" "Gastric antrum"
## [291] "Gastric antrum" "Cardia, NOS"
## [293] "Cardia, NOS" "Cardia, NOS"
## [295] "Gastric antrum" "Body of stomach"
## [297] "Body of stomach" "Cardia, NOS"
## [299] "Gastric antrum" "Gastric antrum"
## [301] "Cardia, NOS" "Gastric antrum"
## [303] "Cardia, NOS" "Gastric antrum"
## [305] "Body of stomach" "Stomach, NOS"
## [307] "Cardia, NOS" "Gastric antrum"
## [309] "Body of stomach" "Gastric antrum"
## [311] "Gastric antrum" "Gastric antrum"
## [313] "Gastric antrum" "Gastric antrum"
## [315] "Body of stomach" "Body of stomach"
## [317] "Body of stomach" "Gastric antrum"
## [319] "Cardia, NOS" "Fundus of stomach"
## [321] "Body of stomach" "Gastric antrum"
## [323] "Gastric antrum" "Gastric antrum"
## [325] "Gastric antrum" "Gastric antrum"
## [327] "Cardia, NOS" "Body of stomach"
## [329] "Gastric antrum" "Cardia, NOS"
## [331] "Gastric antrum" "Gastric antrum"
## [333] "Stomach, NOS" "Body of stomach"
## [335] "Gastric antrum" "Cardia, NOS"
## [337] "Fundus of stomach" "Body of stomach"
## [339] "Body of stomach" "Gastric antrum"
## [341] "Gastric antrum" "Gastric antrum"
## [343] "Fundus of stomach" "Cardia, NOS"
## [345] "Fundus of stomach" "Cardia, NOS"
## [347] "Gastric antrum" "Body of stomach"
## [349] "Cardia, NOS" "Cardia, NOS"
## [351] "Gastric antrum" "Gastric antrum"
## [353] "Fundus of stomach" "Body of stomach"
## [355] "Gastric antrum" "Gastric antrum"
## [357] "Cardia, NOS" "Cardia, NOS"
## [359] "Cardia, NOS" "Gastric antrum"
## [361] "Cardia, NOS" "Cardia, NOS"
## [363] "Cardia, NOS" "Gastric antrum"
## [365] "Cardia, NOS" "Cardia, NOS"
## [367] "Gastric antrum" "Fundus of stomach"
## [369] "Body of stomach" "Cardia, NOS"
## [371] "Body of stomach" "Cardia, NOS"
## [373] "Cardia, NOS" "Fundus of stomach"
## [375] "Gastric antrum" "Body of stomach"
## [377] "Fundus of stomach" "Fundus of stomach"
## [379] "Stomach, NOS" "Gastric antrum"
## [381] "Fundus of stomach" "Gastric antrum"
## [383] "Stomach, NOS" "Gastric antrum"
## [385] "Cardia, NOS" "Gastric antrum"
## [387] "Body of stomach" "Cardia, NOS"
## [389] "Gastric antrum" "Cardia, NOS"
## [391] "Cardia, NOS" "Gastric antrum"
## [393] "Body of stomach" "Body of stomach"
## [395] "Gastric antrum" "Stomach, NOS"
## [397] "Gastric antrum" "Body of stomach"
## [399] "Body of stomach" "Fundus of stomach"
## [401] "Gastric antrum" "Body of stomach"
## [403] "Body of stomach" "Body of stomach"
## [405] "Cardia, NOS" "Gastric antrum"
## [407] "Gastric antrum" "Body of stomach"
## [409] "Cardia, NOS" "Gastric antrum"
## [411] "Gastric antrum" "Fundus of stomach"
## [413] "Cardia, NOS" "Cardia, NOS"
## [415] "Fundus of stomach"rse$gender## [1] "male" "female" "male" "female" "female" "female" "female" "male"
## [9] "male" "female" "male" "female" "male" "male" "female" "male"
## [17] "female" "female" "female" "male" "female" "male" "male" "female"
## [25] "female" "male" "male" "male" "male" "female" "male" "male"
## [33] "male" "female" "male" "male" "male" "male" "male" "male"
## [41] "male" "male" "male" "female" "male" "female" "male" "male"
## [49] "male" "male" "male" "female" "male" "male" "female" "female"
## [57] "male" "female" "female" "male" "male" "male" "male" "male"
## [65] "male" "male" "female" "male" "male" "male" "male" "female"
## [73] "male" "female" "male" "male" "male" "female" "female" "male"
## [81] "male" "female" "male" "male" "male" "male" "female" "male"
## [89] "female" "male" "male" "male" "male" "female" "female" "male"
## [97] "male" "male" "male" "male" "male" "male" "male" "male"
## [105] "male" "male" "male" "male" "female" "male" "male" "male"
## [113] "male" "male" "male" "female" "female" "male" "male" "male"
## [121] "female" "male" "male" "male" "female" "male" "female" "female"
## [129] "male" "female" "female" "male" "female" "female" "female" "male"
## [137] "male" "male" "male" "male" "male" "female" "male" "female"
## [145] "male" "male" "male" "female" "female" "female" "male" "male"
## [153] "male" "male" "male" "female" "male" "female" "female" "male"
## [161] "male" "female" "female" "male" "female" "male" "male" "female"
## [169] "female" "female" "male" "female" "male" "male" "male" "male"
## [177] "female" "male" "male" "female" "male" "male" "male" "male"
## [185] "male" "male" "female" "female" "female" "male" "male" "female"
## [193] "male" "female" "male" "male" "female" "male" "male" "female"
## [201] "male" "male" "female" "female" "male" "female" "male" "male"
## [209] "male" "female" "male" "male" "female" "female" "male" "male"
## [217] "male" "male" "female" "male" "male" "male" "male" "female"
## [225] "male" "female" "male" "male" "male" "male" "male" "male"
## [233] "female" "male" "male" "male" "male" "male" "male" "male"
## [241] "female" "male" "male" "male" "male" "male" "male" "male"
## [249] "female" "male" "female" "male" "female" "female" "male" "female"
## [257] "male" "female" "male" "male" "male" "male" "male" "male"
## [265] "female" "male" "male" "female" "female" "female" "female" "male"
## [273] "male" "female" "female" "male" "female" "female" "female" "female"
## [281] "female" "female" "male" "male" "male" "male" "male" "female"
## [289] "male" "female" "female" "male" "male" "female" "female" "male"
## [297] "male" "male" "male" "male" "male" "male" "male" "male"
## [305] "male" "male" "female" "male" "female" "female" "female" "female"
## [313] "male" "male" "female" "male" "female" "male" "female" "female"
## [321] "male" "male" "female" "male" "female" "female" "male" "female"
## [329] "male" "male" "male" "male" "male" "female" "female" "male"
## [337] "male" "female" "male" "female" "male" "male" "male" "male"
## [345] "male" "female" "female" "female" "male" "male" "male" "male"
## [353] "male" "female" "female" "male" "male" "male" "female" "female"
## [361] "male" "male" "male" "male" "male" "female" "male" "male"
## [369] "male" "female" "male" "male" "female" "female" "male" "female"
## [377] "male" "male" "male" "male" "female" "male" "female" "female"
## [385] "female" "female" "female" "male" "female" "male" "male" "female"
## [393] "female" "male" "male" "male" "male" "male" "male" "male"
## [401] "male" "female" "female" "male" "female" "male" "male" "male"
## [409] "male" "male" "male" "female" "male" "female" "male"rse$paper_Lauren.Class## [1] Mixed Intestinal Intestinal Intestinal Diffuse Diffuse
## [7] Diffuse Intestinal <NA> <NA> Intestinal <NA>
## [13] Intestinal Intestinal <NA> Diffuse Intestinal Intestinal
## [19] Intestinal <NA> <NA> Diffuse <NA> <NA>
## [25] NA Intestinal Intestinal <NA> <NA> <NA>
## [31] Intestinal Mixed <NA> Intestinal Intestinal Diffuse
## [37] Diffuse Intestinal Intestinal Intestinal <NA> Intestinal
## [43] Intestinal <NA> Intestinal <NA> Intestinal Diffuse
## [49] Intestinal <NA> Intestinal Intestinal Diffuse Diffuse
## [55] NA <NA> Mixed <NA> Intestinal <NA>
## [61] <NA> Diffuse Intestinal Intestinal <NA> Mixed
## [67] Intestinal Intestinal Intestinal Intestinal <NA> Diffuse
## [73] Intestinal Intestinal Intestinal Intestinal Intestinal <NA>
## [79] Intestinal <NA> Mixed Diffuse <NA> Diffuse
## [85] <NA> Diffuse <NA> Intestinal Intestinal Intestinal
## [91] Intestinal Intestinal Intestinal <NA> Intestinal Intestinal
## [97] Diffuse Intestinal Diffuse Intestinal Intestinal <NA>
## [103] <NA> Intestinal <NA> Intestinal Diffuse Intestinal
## [109] Mixed <NA> Intestinal Diffuse Diffuse <NA>
## [115] Intestinal Intestinal Intestinal Intestinal Intestinal Diffuse
## [121] Intestinal Intestinal <NA> <NA> Diffuse Diffuse
## [127] NA Intestinal <NA> Diffuse Diffuse Mixed
## [133] <NA> Intestinal Intestinal Diffuse Intestinal <NA>
## [139] Intestinal Intestinal Intestinal Intestinal Intestinal Diffuse
## [145] Intestinal <NA> NA Intestinal Intestinal Mixed
## [151] <NA> <NA> Intestinal Intestinal Intestinal Intestinal
## [157] <NA> Intestinal Intestinal <NA> <NA> Intestinal
## [163] <NA> <NA> Diffuse <NA> Intestinal <NA>
## [169] Mixed <NA> <NA> Diffuse Diffuse <NA>
## [175] Intestinal Diffuse Intestinal <NA> <NA> Intestinal
## [181] <NA> Intestinal <NA> Intestinal NA Diffuse
## [187] <NA> <NA> Intestinal <NA> <NA> <NA>
## [193] Mixed NA Mixed Intestinal <NA> <NA>
## [199] <NA> Diffuse Intestinal Intestinal <NA> Diffuse
## [205] Diffuse <NA> Intestinal <NA> <NA> <NA>
## [211] Intestinal <NA> <NA> Diffuse Intestinal Intestinal
## [217] Diffuse Intestinal <NA> <NA> Intestinal Intestinal
## [223] Diffuse Diffuse Diffuse Intestinal <NA> <NA>
## [229] <NA> Intestinal Intestinal Intestinal <NA> Intestinal
## [235] Diffuse <NA> Intestinal Diffuse Intestinal Mixed
## [241] Diffuse Intestinal <NA> Intestinal Intestinal Intestinal
## [247] <NA> Diffuse Diffuse <NA> Mixed <NA>
## [253] Mixed Intestinal Intestinal Intestinal Intestinal Diffuse
## [259] <NA> Diffuse Intestinal Intestinal Intestinal <NA>
## [265] Diffuse Intestinal <NA> Diffuse <NA> <NA>
## [271] <NA> <NA> <NA> Intestinal Intestinal <NA>
## [277] Intestinal NA <NA> <NA> <NA> NA
## [283] <NA> Intestinal <NA> <NA> <NA> <NA>
## [289] <NA> Mixed Intestinal <NA> <NA> <NA>
## [295] Diffuse Intestinal Intestinal <NA> Intestinal <NA>
## [301] Intestinal <NA> Intestinal Diffuse <NA> <NA>
## [307] <NA> Intestinal Intestinal Intestinal Diffuse Intestinal
## [313] <NA> Intestinal Intestinal Intestinal Intestinal <NA>
## [319] Intestinal Diffuse Intestinal Intestinal <NA> Intestinal
## [325] Intestinal Diffuse Intestinal Intestinal Intestinal <NA>
## [331] Diffuse <NA> Diffuse Diffuse Intestinal Intestinal
## [337] <NA> Intestinal Intestinal Intestinal Intestinal Intestinal
## [343] Mixed Intestinal Intestinal <NA> NA Intestinal
## [349] <NA> <NA> Mixed Diffuse <NA> Diffuse
## [355] Intestinal Intestinal Diffuse <NA> <NA> Intestinal
## [361] <NA> Intestinal <NA> Diffuse <NA> <NA>
## [367] Intestinal NA <NA> Intestinal Intestinal <NA>
## [373] Diffuse Intestinal Intestinal Intestinal <NA> Diffuse
## [379] <NA> <NA> NA Intestinal <NA> Intestinal
## [385] <NA> Intestinal Intestinal <NA> Intestinal <NA>
## [391] <NA> Diffuse Diffuse <NA> <NA> <NA>
## [397] Intestinal Intestinal Intestinal Intestinal Intestinal Intestinal
## [403] Intestinal Intestinal Intestinal Mixed Intestinal Intestinal
## [409] Diffuse Mixed Intestinal Intestinal Intestinal <NA>
## [415] Intestinal
## Levels: Diffuse Intestinal Mixed NArse$paper_Age.at.Initial.Diagnosis## [1] 74.82 58.62 54.93 53.84 53.82 67 56.92 59.86 <NA> <NA> 75.42 <NA>
## [13] 59.19 81.33 <NA> 78.9 75.56 70.8 71.98 <NA> <NA> 82.99 <NA> <NA>
## [25] 66.42 60.79 62.4 <NA> <NA> <NA> 76.84 63.12 <NA> 63.2 67.06 75.55
## [37] 53.47 59.49 74.24 73.32 <NA> 65.15 75.55 <NA> 57.06 <NA> 58.35 83.17
## [49] 64.3 <NA> 72.48 76.8 64.64 55.19 64.25 <NA> 62.15 <NA> 73.02 <NA>
## [61] <NA> 62.65 45.55 87.68 <NA> 62.8 70.28 49.58 69.26 62.4 <NA> 69.09
## [73] 69.83 54.36 68.12 49.1 80.46 <NA> 69.21 <NA> 75.87 66.95 <NA> 69.22
## [85] <NA> 39.58 <NA> 68.17 82.62 77.46 49.19 70.76 76.69 <NA> 51 66.74
## [97] 60.22 65.48 47.95 59.79 79.63 <NA> <NA> 79.97 <NA> 52.8 58.77 72.31
## [109] 71.91 <NA> 51.2 72.05 70.89 <NA> 63.25 72.56 67.02 83.58 50.39 51.98
## [121] 78.07 58.3 <NA> <NA> 50.7 54.93 60.77 78.93 <NA> 76.37 74.41 70.03
## [133] <NA> NA 72.1 58.11 57.33 <NA> 70.61 71.82 61.02 71.97 79.55 76.97
## [145] 73.92 <NA> 77.49 62.5 71.45 54.8 <NA> <NA> 53.09 62.83 65.65 53.85
## [157] <NA> 66.68 75.34 <NA> <NA> 70.99 <NA> <NA> 43.77 <NA> 57.14 <NA>
## [169] 71.31 <NA> <NA> 51.19 60.06 <NA> 74.01 48.08 58.92 <NA> <NA> 72.4
## [181] <NA> 90 <NA> 55.16 56.75 65.1 <NA> <NA> 86.75 <NA> <NA> <NA>
## [193] 80.06 71.18 79.75 74.49 <NA> <NA> <NA> 69.6 57.08 76.76 <NA> 70.43
## [205] 69.47 <NA> 69.67 <NA> <NA> <NA> 49.75 <NA> <NA> 54.07 68.66 66.22
## [217] 41.69 70.08 <NA> <NA> NA 72.72 71.66 63.34 65.7 64.1 <NA> <NA>
## [229] <NA> 77.24 58.16 61.83 <NA> 57.39 69.53 <NA> 84.92 68.92 71.73 68.53
## [241] 61.45 75.31 <NA> 62.21 63.92 61.02 <NA> 61.74 67.59 <NA> 68.02 <NA>
## [253] 80.48 58.66 77.25 64.07 56.33 72.58 <NA> 56.49 73.1 69 81.34 <NA>
## [265] 42.13 90 <NA> 78.33 <NA> <NA> <NA> <NA> <NA> 73.49 60.93 <NA>
## [277] 80.49 73.86 <NA> <NA> <NA> 68.92 <NA> 90 <NA> <NA> <NA> <NA>
## [289] <NA> 72.62 82.15 <NA> <NA> <NA> 34.5 74.17 65.05 <NA> 56.67 <NA>
## [301] 58.11 <NA> 76.71 72.79 <NA> <NA> <NA> 57.79 64.08 66.04 74.53 79.43
## [313] <NA> 70.9 54.66 65.33 78.75 <NA> 67 55.24 76.42 53.3 <NA> 52.47
## [325] 67.73 45.71 83.42 57.68 59.5 <NA> 55.01 <NA> 43.98 68.65 79.95 69.91
## [337] <NA> 74.71 70.19 71.88 72.88 45.97 55.97 58.87 63.65 <NA> 78.77 67.77
## [349] <NA> <NA> 59.58 45.27 <NA> 72.68 74.87 73.99 59.05 <NA> <NA> 58.85
## [361] <NA> 56.79 <NA> 58.91 <NA> <NA> 69.06 51.59 <NA> 68.41 75.22 <NA>
## [373] 53.13 65.01 NA 69.34 <NA> 52 <NA> <NA> 84.53 74.65 <NA> 70.95
## [385] <NA> 71.82 70.68 <NA> 62.18 <NA> <NA> 60.58 46.9 <NA> <NA> <NA>
## [397] 85.83 77.25 75.37 60.05 80.6 58.94 70.67 63.36 81.42 78 63.7 68.42
## [409] 58.75 51.18 56.71 90 44.22 <NA> 59.03
## 278 Levels: 34.5 39.58 41.69 41.93 42.13 43.77 43.98 44.22 45.27 45.55 ... NArse$paper_ARID1A.mutation## [1] 1 0 1 1 0 0 1 1 <NA> <NA> 0 <NA> 0 0 <NA>
## [16] NA 1 1 0 <NA> <NA> 0 <NA> <NA> 1 0 1 <NA> <NA> <NA>
## [31] 0 0 <NA> 0 0 0 1 0 0 1 <NA> NA 0 <NA> 0
## [46] <NA> 0 1 0 <NA> 1 0 1 0 1 <NA> 1 <NA> 1 <NA>
## [61] <NA> 0 1 0 <NA> 0 0 NA 1 0 <NA> 1 0 0 0
## [76] 0 0 <NA> 0 <NA> 0 0 <NA> 0 <NA> 0 <NA> 1 0 1
## [91] 0 0 0 <NA> 0 0 0 1 0 0 1 <NA> <NA> 0 <NA>
## [106] 0 0 0 1 <NA> 0 0 0 <NA> 0 0 0 0 0 1
## [121] 0 0 <NA> <NA> 0 0 1 1 <NA> 0 1 0 <NA> 0 0
## [136] 0 0 <NA> 1 0 0 0 1 0 1 <NA> 1 0 1 0
## [151] <NA> <NA> 0 0 0 1 <NA> 1 0 <NA> <NA> 0 <NA> <NA> 0
## [166] <NA> 0 <NA> 1 <NA> <NA> 1 0 <NA> 0 0 0 <NA> <NA> 0
## [181] <NA> 1 <NA> 1 1 1 <NA> <NA> 0 <NA> <NA> <NA> 0 1 1
## [196] 1 <NA> <NA> <NA> 1 0 0 <NA> 1 1 <NA> 0 <NA> <NA> <NA>
## [211] 0 <NA> <NA> 0 0 0 0 1 <NA> <NA> 0 0 0 0 0
## [226] 0 <NA> <NA> <NA> 0 1 0 <NA> 0 0 <NA> 0 0 1 0
## [241] 0 0 <NA> 0 1 1 <NA> 0 0 <NA> 0 <NA> 0 0 0
## [256] 1 0 0 <NA> 0 0 0 0 <NA> 0 1 <NA> 1 <NA> <NA>
## [271] <NA> <NA> <NA> 0 0 <NA> 1 1 <NA> <NA> <NA> 0 <NA> 0 <NA>
## [286] <NA> <NA> <NA> <NA> 1 0 <NA> <NA> <NA> 0 1 0 <NA> 0 <NA>
## [301] 0 <NA> 1 0 <NA> <NA> <NA> 0 0 1 1 0 <NA> 0 0
## [316] 0 0 <NA> 1 0 0 0 <NA> 0 1 0 1 0 0 <NA>
## [331] NA <NA> 0 0 0 0 <NA> 1 0 1 0 0 0 0 1
## [346] <NA> 1 1 <NA> <NA> 0 0 <NA> 0 1 1 0 <NA> <NA> 0
## [361] <NA> 0 <NA> 0 <NA> <NA> 0 1 <NA> 1 1 <NA> 0 0 1
## [376] 0 <NA> 0 <NA> <NA> 1 0 <NA> 1 <NA> 0 0 <NA> 0 <NA>
## [391] <NA> 0 0 <NA> <NA> <NA> 1 0 1 1 1 0 0 0 0
## [406] 1 1 0 0 0 NA 0 0 <NA> 0
## Levels: 0 1 NArse$paper_CDKN2A.Epigenetically.Silenced## [1] false false false false false true true true <NA> <NA> false <NA>
## [13] NA NA <NA> NA NA true NA <NA> <NA> false <NA> <NA>
## [25] NA true true <NA> <NA> <NA> NA true <NA> true false false
## [37] true false false false <NA> true false <NA> NA <NA> true false
## [49] false <NA> false false true true true <NA> false <NA> NA <NA>
## [61] <NA> false false NA <NA> false false NA NA false <NA> NA
## [73] NA NA false false false <NA> false <NA> false true <NA> false
## [85] <NA> true <NA> false true true false true NA <NA> false false
## [97] false false false false false <NA> <NA> false <NA> false false false
## [109] NA <NA> NA true false <NA> true NA false false true false
## [121] NA NA <NA> <NA> false false NA true <NA> NA NA NA
## [133] <NA> false false false NA <NA> true false true false true false
## [145] false <NA> true false true false <NA> <NA> false false false true
## [157] <NA> NA NA <NA> <NA> true <NA> <NA> false <NA> false <NA>
## [169] true <NA> <NA> false false <NA> false false true <NA> <NA> false
## [181] <NA> true <NA> true true false <NA> <NA> false <NA> <NA> <NA>
## [193] true true false true <NA> <NA> <NA> true false false <NA> false
## [205] true <NA> false <NA> <NA> <NA> false <NA> <NA> false false NA
## [217] false NA <NA> <NA> false NA false false NA false <NA> <NA>
## [229] <NA> false false false <NA> true false <NA> NA false NA NA
## [241] false NA <NA> true true false <NA> false NA <NA> false <NA>
## [253] true NA false true NA NA <NA> NA false true true <NA>
## [265] false NA <NA> false <NA> <NA> <NA> <NA> <NA> false NA <NA>
## [277] NA true <NA> <NA> <NA> NA <NA> false <NA> <NA> <NA> <NA>
## [289] <NA> false NA <NA> <NA> <NA> false false NA <NA> NA <NA>
## [301] true <NA> true false <NA> <NA> <NA> false false false false NA
## [313] <NA> false false false false <NA> false false NA false <NA> true
## [325] false false true false false <NA> false <NA> NA true false true
## [337] <NA> false true false false true false false true <NA> NA true
## [349] <NA> <NA> false false <NA> false NA false false <NA> <NA> false
## [361] <NA> false <NA> false <NA> <NA> false true <NA> true false <NA>
## [373] false false true true <NA> false <NA> <NA> false false <NA> false
## [385] <NA> true false <NA> false <NA> <NA> false false <NA> <NA> <NA>
## [397] NA false true true NA NA false false NA true false NA
## [409] false false false false true <NA> false
## Levels: false NA truerse$paper_Country## [1] Vietnam Russia Korea_South Korea_South Russia
## [6] Germany Korea_South Russia <NA> <NA>
## [11] Vietnam <NA> Ukraine Germany <NA>
## [16] Russia Ukraine Russia Russia <NA>
## [21] <NA> Vietnam <NA> <NA> Russia
## [26] Russia Russia <NA> <NA> <NA>
## [31] Germany Ukraine <NA> Russia Russia
## [36] Poland Poland Russia United_States Poland
## [41] <NA> Russia Korea_South <NA> Vietnam
## [46] <NA> Vietnam Germany Poland <NA>
## [51] Russia Ukraine Ukraine Ukraine Ukraine
## [56] <NA> Ukraine <NA> Russia <NA>
## [61] <NA> Ukraine Vietnam Russia <NA>
## [66] Russia Russia Germany Germany Poland
## [71] <NA> Germany Germany Ukraine Vietnam
## [76] Vietnam Poland <NA> Ukraine <NA>
## [81] Poland Vietnam <NA> Ukraine <NA>
## [86] Vietnam <NA> United_States Korea_South Korea_South
## [91] Russia United_States Korea_South <NA> Vietnam
## [96] Germany Vietnam Russia Vietnam Ukraine
## [101] United_States <NA> <NA> United_States <NA>
## [106] Vietnam Poland Russia United_States <NA>
## [111] Russia Korea_South Vietnam <NA> Russia
## [116] Vietnam Poland Germany United_States Vietnam
## [121] Russia Russia <NA> <NA> Russia
## [126] Russia Russia Russia <NA> Russia
## [131] Russia Ukraine <NA> Canada Russia
## [136] Russia Germany <NA> Korea_South Korea_South
## [141] Poland United_States Russia Korea_South Germany
## [146] <NA> United_States Russia Russia Poland
## [151] <NA> <NA> Poland United_States Vietnam
## [156] Poland <NA> Russia Germany <NA>
## [161] <NA> Ukraine <NA> <NA> Vietnam
## [166] <NA> Poland <NA> Ukraine <NA>
## [171] <NA> Russia Russia <NA> Ukraine
## [176] United_States Korea_South <NA> <NA> Korea_South
## [181] <NA> United_States <NA> United_States Russia
## [186] Poland <NA> <NA> Vietnam <NA>
## [191] <NA> <NA> United_States Russia United_States
## [196] Korea_South <NA> <NA> <NA> Poland
## [201] Russia Russia <NA> Ukraine Vietnam
## [206] <NA> Ukraine <NA> <NA> <NA>
## [211] United_States <NA> <NA> Russia Germany
## [216] Korea_South Vietnam Germany <NA> <NA>
## [221] Canada Russia Germany Russia Ukraine
## [226] Poland <NA> <NA> <NA> Russia
## [231] Germany Russia <NA> Poland Ukraine
## [236] <NA> Germany United_States Korea_South United_States
## [241] Vietnam Russia <NA> Vietnam Russia
## [246] Korea_South <NA> Russia Germany <NA>
## [251] Russia <NA> Ukraine Germany United_States
## [256] Ukraine Germany Germany <NA> Russia
## [261] Korea_South Vietnam Russia <NA> Russia
## [266] Germany <NA> Vietnam <NA> <NA>
## [271] <NA> <NA> <NA> Vietnam Russia
## [276] <NA> Russia Russia <NA> <NA>
## [281] <NA> Germany <NA> Vietnam <NA>
## [286] <NA> <NA> <NA> <NA> Russia
## [291] Vietnam <NA> <NA> <NA> Vietnam
## [296] Russia Russia <NA> Korea_South <NA>
## [301] Poland <NA> Vietnam Poland <NA>
## [306] <NA> <NA> Vietnam Russia Poland
## [311] Ukraine Russia <NA> United_States Germany
## [316] Russia Germany <NA> Russia Russia
## [321] Germany Poland <NA> Vietnam Ukraine
## [326] Vietnam Germany Ukraine Ukraine <NA>
## [331] Ukraine <NA> Russia Ukraine Vietnam
## [336] United_States <NA> Russia Russia Korea_South
## [341] Poland Korea_South Ukraine Russia Poland
## [346] <NA> Russia Korea_South <NA> <NA>
## [351] Germany Vietnam <NA> Russia Russia
## [356] Korea_South United_States <NA> <NA> Korea_South
## [361] <NA> Poland <NA> Vietnam <NA>
## [366] <NA> Korea_South Ukraine <NA> Russia
## [371] Korea_South <NA> Ukraine Ukraine Canada
## [376] Russia <NA> Vietnam <NA> <NA>
## [381] Ukraine Korea_South <NA> Korea_South <NA>
## [386] Korea_South Poland <NA> Korea_South <NA>
## [391] <NA> Poland Russia <NA> <NA>
## [396] <NA> Germany Poland Ukraine Vietnam
## [401] Russia Russia Poland Poland Germany
## [406] United_States Vietnam Germany Germany Vietnam
## [411] Vietnam Russia Poland <NA> Vietnam
## 8 Levels: Canada Germany Korea_South Poland Russia Ukraine ... Vietnamrse$paper_Days.to.Death## [1] NA NA NA NA NA NA NA 422 <NA> <NA> 292 <NA> NA NA <NA>
## [16] NA NA NA NA <NA> <NA> NA <NA> <NA> NA NA NA <NA> <NA> <NA>
## [31] NA 518 <NA> NA 279 NA NA NA NA NA <NA> NA NA <NA> NA
## [46] <NA> NA NA NA <NA> 439 NA NA NA NA <NA> 466 <NA> NA <NA>
## [61] <NA> 350 NA NA <NA> NA NA NA NA 312 <NA> 273 NA NA NA
## [76] NA NA <NA> NA <NA> NA NA <NA> NA <NA> NA <NA> NA NA NA
## [91] NA NA NA <NA> NA 2100 NA NA NA NA NA <NA> <NA> 2197 <NA>
## [106] NA NA NA 777 <NA> 187 NA NA <NA> NA NA NA 426 NA 98
## [121] 201 NA <NA> <NA> NA NA NA NA <NA> NA NA NA <NA> NA NA
## [136] NA NA <NA> NA NA NA 243 NA NA 850 <NA> NA NA NA 445
## [151] <NA> <NA> NA NA NA NA <NA> 940 NA <NA> <NA> NA <NA> <NA> NA
## [166] <NA> NA <NA> NA <NA> <NA> NA NA <NA> 82 153 NA <NA> <NA> NA
## [181] <NA> NA <NA> NA NA NA <NA> <NA> NA <NA> <NA> <NA> NA NA NA
## [196] NA <NA> <NA> <NA> NA 81 NA <NA> 448 NA <NA> NA <NA> <NA> <NA>
## [211] 1796 <NA> <NA> NA 243 180 NA 215 <NA> <NA> NA NA 0 NA NA
## [226] NA <NA> <NA> <NA> NA NA NA <NA> NA NA <NA> NA 20 3 128
## [241] NA NA <NA> NA NA NA <NA> NA NA <NA> NA <NA> NA NA 99
## [256] NA NA 0 <NA> 141 NA 386 NA <NA> NA 31 <NA> NA <NA> <NA>
## [271] <NA> <NA> <NA> NA NA <NA> NA NA <NA> <NA> <NA> 122 <NA> NA <NA>
## [286] <NA> <NA> <NA> <NA> 245 NA <NA> <NA> <NA> NA NA NA <NA> NA <NA>
## [301] 406 <NA> NA NA <NA> <NA> <NA> NA NA NA NA NA <NA> NA NA
## [316] NA 1095 <NA> NA NA NA NA <NA> NA NA NA NA 558 NA <NA>
## [331] NA <NA> 291 741 NA NA <NA> 525 NA NA NA NA NA NA NA
## [346] <NA> NA NA <NA> <NA> 335 NA <NA> 291 NA NA 105 <NA> <NA> NA
## [361] <NA> NA <NA> NA <NA> <NA> NA NA <NA> NA NA <NA> NA NA NA
## [376] NA <NA> NA <NA> <NA> NA NA <NA> NA <NA> NA NA <NA> NA <NA>
## [391] <NA> NA NA <NA> <NA> <NA> NA NA NA NA NA NA NA NA NA
## [406] 335 5 NA 211 NA NA NA NA <NA> NA
## 52 Levels: 0 10 105 1095 122 128 141 153 16 1796 180 187 20 201 2100 ... NArse$paper_Days.to.Last.Follow.up## [1] 0 21 170 544 537 0 595 399 <NA> <NA> 10 <NA> 202 580 <NA>
## [16] 0 0 373 0 <NA> <NA> 61 <NA> <NA> 0 388 356 <NA> <NA> <NA>
## [31] 699 372 <NA> 5 19 582 543 569 76 508 <NA> 11 23 <NA> 0
## [46] <NA> 386 3196 353 <NA> 25 407 3 7 423 <NA> 5 <NA> 0 <NA>
## [61] <NA> 3 468 0 <NA> 65 51 365 485 312 <NA> NA 0 308 0
## [76] 6 385 <NA> 0 <NA> 6 0 <NA> 99 <NA> 6 <NA> 17 368 270
## [91] 394 591 431 <NA> 406 1674 0 23 389 432 412 <NA> <NA> NA <NA>
## [106] 0 566 22 NA <NA> 0 64 413 <NA> 21 0 523 NA 645 5
## [121] 0 0 <NA> <NA> 21 484 0 257 <NA> 0 0 377 <NA> 0 42
## [136] 23 242 <NA> 323 176 104 237 414 8 NA <NA> 569 468 331 211
## [151] <NA> <NA> 321 372 0 383 <NA> 0 92 <NA> <NA> 0 <NA> <NA> 0
## [166] <NA> 516 <NA> 0 <NA> <NA> 171 679 <NA> 6 NA 347 <NA> <NA> 143
## [181] <NA> 171 <NA> 307 480 564 <NA> <NA> 0 <NA> <NA> <NA> 524 12 485
## [196] 374 <NA> <NA> <NA> 180 8 5 <NA> 5 468 <NA> 240 <NA> <NA> <NA>
## [211] NA <NA> <NA> 565 NA NA 0 NA <NA> <NA> 0 0 NA 12 0
## [226] 603 <NA> <NA> <NA> 28 182 21 <NA> 592 411 <NA> 822 NA NA 7
## [241] 0 0 <NA> 0 582 912 <NA> 331 0 <NA> 9 <NA> 17 942 5
## [256] 12 1644 NA <NA> 0 809 386 438 <NA> 674 NA <NA> 0 <NA> <NA>
## [271] <NA> <NA> <NA> 0 47 <NA> 0 10 <NA> <NA> <NA> NA <NA> 0 <NA>
## [286] <NA> <NA> <NA> <NA> 22 0 <NA> <NA> <NA> 396 378 0 <NA> 692 <NA>
## [301] 406 <NA> 0 528 <NA> <NA> <NA> 6 378 126 0 0 <NA> 455 0
## [316] 469 31 <NA> 25 23 1431 573 <NA> 459 472 6 245 183 0 <NA>
## [331] 0 <NA> 0 383 0 594 <NA> 308 642 360 131 462 390 0 449
## [346] <NA> 0 736 <NA> <NA> NA 78 <NA> 15 0 190 NA <NA> <NA> 400
## [361] <NA> 379 <NA> 0 <NA> <NA> 785 0 <NA> 0 358 <NA> 369 429 0
## [376] 475 <NA> 0 <NA> <NA> 92 99 <NA> 310 <NA> 198 463 <NA> 253 <NA>
## [391] <NA> 119 286 <NA> <NA> <NA> 0 354 338 0 0 45 465 403 576
## [406] 0 NA 912 NA 0 383 614 741 <NA> 0
## 159 Levels: 0 1 10 104 11 119 12 122 126 131 143 1431 15 16 1644 1674 17 ... NA#BCR Biotab for clinical tcga
querycli_STAD<-GDCquery(project = "TCGA-STAD",
data.category = "Clinical",
data.type = "Clinical Supplement",
data.format = "BCR Biotab")
GDCdownload(querycli_STAD)
clinical.BCRtab.STAD <- GDCprepare(querycli_STAD)##
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|======================================================================| 100%# All available tables
names(clinical.BCRtab.STAD)## [1] "clinical_patient_stad" "clinical_nte_stad"
## [3] "clinical_omf_v4.0_stad" "clinical_radiation_stad"
## [5] "clinical_drug_stad" "clinical_follow_up_v1.0_stad"# colnames from clinical_patient_stad
tibble::tibble(sort(colnames(clinical.BCRtab.STAD$clinical_patient_stad)))## # A tibble: 63 x 1
## `sort(colnames(clinical.BCRtab.STAD$clinical_patient_stad))`
## <chr>
## 1 age_at_initial_pathologic_diagnosis
## 2 ajcc_metastasis_pathologic_pm
## 3 ajcc_nodes_pathologic_pn
## 4 ajcc_pathologic_tumor_stage
## 5 ajcc_staging_edition
## 6 ajcc_tumor_pathologic_pt
## 7 anatomic_neoplasm_subdivision
## 8 anatomic_neoplasm_subdivision_other
## 9 antireflux_treatment
## 10 antireflux_treatment_type
## # ... with 53 more rows# pathologic tuimor stage status count
plyr::count(clinical.BCRtab.STAD$clinical_patient_stad$ajcc_pathologic_tumor_stage) ## x freq
## 1 [Discrepancy] 11
## 2 [Not Available] 16
## 3 CDE_ID:3203222 1
## 4 pathologic_stage 1
## 5 Stage I 2
## 6 Stage IA 16
## 7 Stage IB 41
## 8 Stage II 33
## 9 Stage IIA 41
## 10 Stage IIB 56
## 11 Stage III 3
## 12 Stage IIIA 79
## 13 Stage IIIB 63
## 14 Stage IIIC 38
## 15 Stage IV 44# subset for custom clinical for me
barcode<-data.frame(rse$paper_patient)
sex<-data.frame(rse$paper_Gender)
T_stage<-data.frame(rse$paper_Pathologic.T)
N_stage<-data.frame(rse$paper_Pathologic.N)
M_stage<-data.frame(rse$paper_Pathologic.M)
TCGA_sub<-data.frame(rse$paper_Molecular.Subtype)
lauren_sub<-data.frame(rse$paper_Lauren.Class)
age<-data.frame(rse$paper_Age.at.Initial.Diagnosis)
vital_sta<-data.frame(rse$paper_Vital.Status)
Days.to.Death<-data.frame(rse$paper_Days.to.Death)
Days.to.Last.Follow.up<-data.frame(rse$paper_Days.to.Last.Follow.up)
Days.to.Recurrence<-data.frame(rse$paper_Days.to.Recurrence)
ARID1A_mut<-data.frame(rse$paper_ARID1A.mutation)
KRAS_mut<-data.frame(rse$paper_KRAS.mutation)
PIK3CA_mut<-data.frame(rse$paper_PIK3CA.mutation)
RHOA_mut<-data.frame(rse$paper_RHOA.mutation)
TP53_mut<-data.frame(rse$paper_TP53.mutation)
customeclinSTAD<-cbind(barcode,
sex,
T_stage,
N_stage,
M_stage,
TCGA_sub,
lauren_sub,
age,
vital_sta,
Days.to.Death,
Days.to.Last.Follow.up,
Days.to.Recurrence,
ARID1A_mut,
KRAS_mut,
PIK3CA_mut,
RHOA_mut,
TP53_mut)
write.csv(customeclinSTAD,"custom clinical STAD ok.csv")
#from both custom clinival csv and dataFilt STAD csv, analyze using excel (best)####subtype only TCGA tumor############
sub_TCGA<-read.csv("only tumor TCGA norm counts for graph subtype (add rse paper lauren and tcga sub).csv",sep="\t")
head(sub_TCGA)## Patient.ID C2orf34 FAM86A log2.CAMKMT log2.FAM86A Q.CAMKMT Q.FAM86A
## 1 TCGA-3M-AB46 519 1847 9.019591 10.850968 High CAMKMT High FAM86A
## 2 TCGA-3M-AB47 280 919 8.129283 9.843921
## 3 TCGA-B7-5816 382 943 8.577429 9.881114
## 4 TCGA-B7-5818 668 794 9.383704 9.632995 High CAMKMT
## 5 TCGA-B7-A5TI 323 1041 8.335390 10.023754
## 6 TCGA-B7-A5TJ 707 1242 9.465566 10.278449 High CAMKMT High FAM86A
## M.CAMKMT M.FAM86A T N M Stage days_to_last_follow_up
## 1 High CAMKMT High FAM86A T2b N0 Stage IB 1765
## 2 Low CAMKMT High FAM86A T3 N2 Stage IIIB NA
## 3 High CAMKMT High FAM86A T4a N0 M0 Stage IIB 812
## 4 High CAMKMT Low FAM86A T2 N0 M0 Stage IB 356
## 5 Low CAMKMT High FAM86A T4 N3 M0 Stage IIIC 595
## 6 High CAMKMT High FAM86A T4a M0 Stage IIB 335
## vital_status Mol..Sub Lauren
## 1 Alive
## 2 Dead
## 3 Alive MSI Diffuse
## 4 Alive EBV Intestinal
## 5 Alive
## 6 Alive#by stage
sub_TCGA<-sub_TCGA %>%
mutate(Stage2 = case_when(Stage == 'Stage I' ~ 'Stage I',
Stage == 'Stage IA' ~ 'Stage I',
Stage == 'Stage IB' ~ 'Stage I',
Stage == 'Stage II' ~ 'Stage II',
Stage == 'Stage IIA' ~ 'Stage II',
Stage == 'Stage IIB' ~ 'Stage II',
Stage == 'Stage III' ~ 'Stage III',
Stage == 'Stage IIIA' ~ 'Stage III',
Stage == 'Stage IIIB' ~ 'Stage III',
Stage == 'Stage IIIC' ~ 'Stage III',
Stage == 'Stage IV' ~ 'Stage IV'))
View(sub_TCGA)
ggplot(data=subset(sub_TCGA, !is.na(Stage2)),aes(x=Stage2,y=log2.FAM86A,fill=Stage2))+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text = element_text(family = "Arial",color="black"),
axis.title.y = element_text(vjust = 2.5),
axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
legend.position = 'none',
aspect.ratio = 1.5,
panel.grid.major.x = element_blank())+
labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)
ggsave('FAM86A tcga by stage.svg',dpi=300, width=4,units = "in")
kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559pairwise.wilcox.test(sub_TCGA$log2.FAM86A, sub_TCGA$Stage2,paired=FALSE,
p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: sub_TCGA$log2.FAM86A and sub_TCGA$Stage2
##
## Stage I Stage II Stage III
## Stage II 0.99 - -
## Stage III 0.57 0.38 -
## Stage IV 0.68 0.68 0.38
##
## P value adjustment method: BH#by T
sub_TCGA<-sub_TCGA %>%
mutate(T2 = case_when(T == 'T1' ~ 'T1',
T == 'T1a' ~ 'T1',
T == 'T1b' ~ 'T1',
T == 'T2' ~ 'T2',
T == 'T2a' ~ 'T2',
T == 'T2b' ~ 'T2',
T == 'T3' ~ 'T3',
T == 'T4' ~ 'T4',
T == 'T4a' ~ 'T4',
T == 'T4b' ~ 'T4'))
ggplot(data=subset(sub_TCGA, !is.na(T2)),aes(x=T2,y=log2.FAM86A,fill=T2))+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text = element_text(family = "Arial",color="black"),
axis.title.y = element_text(vjust = 2.5),
axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
legend.position = 'none',
aspect.ratio = 1.5,
panel.grid.major.x = element_blank())+
labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)
ggsave('FAM86A tcga by Tstage.svg',dpi=300, width=4,units = "in")
kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559pairwise.wilcox.test(sub_TCGA$log2.FAM86A, sub_TCGA$Stage2,paired=FALSE,
p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: sub_TCGA$log2.FAM86A and sub_TCGA$Stage2
##
## Stage I Stage II Stage III
## Stage II 0.99 - -
## Stage III 0.57 0.38 -
## Stage IV 0.68 0.68 0.38
##
## P value adjustment method: BH#by N
sub_TCGA<-sub_TCGA %>%
mutate(N2 = case_when(N == 'N0' ~ 'N0',
N == 'N1' ~ 'N1',
N == 'N2' ~ 'N2',
N == 'N3' ~ 'N3',
N == 'N3a' ~ 'N3',
N == 'N3b' ~ 'N3'))
ggplot(data=subset(sub_TCGA, !is.na(N2)),aes(x=N2,y=log2.FAM86A,fill=N2))+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text = element_text(family = "Arial",color="black"),
axis.title.y = element_text(vjust = 2.5),
axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
legend.position = 'none',
aspect.ratio = 1.5,
panel.grid.major.x = element_blank())+
labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)
ggsave('FAM86A tcga by Nstage.svg',dpi=300, width=4,units = "in")
kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559pairwise.wilcox.test(sub_TCGA$log2.FAM86A, sub_TCGA$Stage2,paired=FALSE,
p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: sub_TCGA$log2.FAM86A and sub_TCGA$Stage2
##
## Stage I Stage II Stage III
## Stage II 0.99 - -
## Stage III 0.57 0.38 -
## Stage IV 0.68 0.68 0.38
##
## P value adjustment method: BHggsave('FAM86A TCGA N.png',dpi=500,units = "px",width=1250)
#by M
sub_TCGA<-sub_TCGA %>%
mutate(M2 = case_when(M == 'M0' ~ 'M0',
M == 'M1' ~ 'M1'))
ggplot(data=subset(sub_TCGA, !is.na(M2)),aes(x=M2,y=log2.FAM86A,fill=M2))+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text = element_text(family = "Arial",color="black"),
axis.title.y = element_text(vjust = 2.5),
axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
legend.position = 'none',
aspect.ratio = 1.85,
panel.grid.major.x = element_blank())+
labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)
ggsave('FAM86A tcga by Mstage.svg',dpi=300, width=4,units = "in")
ggsave('FAM86A TCGA M.png',dpi=500,width = 1400,height = 1734,units = "px")
#save edited csv
write.csv(sub_TCGA,"subtype TCGA STAD plot subtypes.csv")
#statistic subtypes kruskal wallis
kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559kruskal.test(log2.FAM86A ~ T2, data = sub_TCGA)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by T2
## Kruskal-Wallis chi-squared = 0.073071, df = 3, p-value = 0.9949kruskal.test(log2.FAM86A ~ N2, data = sub_TCGA)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by N2
## Kruskal-Wallis chi-squared = 1.3156, df = 3, p-value = 0.7254wilcox.test(log2.FAM86A ~ M2, data = sub_TCGA)##
## Wilcoxon rank sum test with continuity correction
##
## data: log2.FAM86A by M2
## W = 4209.5, p-value = 0.1924
## alternative hypothesis: true location shift is not equal to 0#addition subtype based on rse paper
#lauren
sub_rse<-read.csv("only tumor TCGA norm counts for graph subtype (add rse paper lauren and tcga sub).csv",sep='\t')
head(sub_rse)## Patient.ID C2orf34 FAM86A log2.CAMKMT log2.FAM86A Q.CAMKMT Q.FAM86A
## 1 TCGA-3M-AB46 519 1847 9.019591 10.850968 High CAMKMT High FAM86A
## 2 TCGA-3M-AB47 280 919 8.129283 9.843921
## 3 TCGA-B7-5816 382 943 8.577429 9.881114
## 4 TCGA-B7-5818 668 794 9.383704 9.632995 High CAMKMT
## 5 TCGA-B7-A5TI 323 1041 8.335390 10.023754
## 6 TCGA-B7-A5TJ 707 1242 9.465566 10.278449 High CAMKMT High FAM86A
## M.CAMKMT M.FAM86A T N M Stage days_to_last_follow_up
## 1 High CAMKMT High FAM86A T2b N0 Stage IB 1765
## 2 Low CAMKMT High FAM86A T3 N2 Stage IIIB NA
## 3 High CAMKMT High FAM86A T4a N0 M0 Stage IIB 812
## 4 High CAMKMT Low FAM86A T2 N0 M0 Stage IB 356
## 5 Low CAMKMT High FAM86A T4 N3 M0 Stage IIIC 595
## 6 High CAMKMT High FAM86A T4a M0 Stage IIB 335
## vital_status Mol..Sub Lauren
## 1 Alive
## 2 Dead
## 3 Alive MSI Diffuse
## 4 Alive EBV Intestinal
## 5 Alive
## 6 Alivesub_rse<-sub_rse %>%
mutate(Lauren2 = case_when(Lauren == 'Diffuse' ~ 'Diffuse',
Lauren == 'Intestinal' ~ 'Intestinal',
Lauren == 'Mixed' ~ 'Mixed'))
ggplot(data=subset(sub_rse, !is.na(Lauren2)),aes(x=Lauren2,y=log2.FAM86A,fill=Lauren2))+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text = element_text(family = "Arial",color="black"),
axis.title.y = element_text(vjust = 2.5),
axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
legend.position = 'none',
aspect.ratio = 1.85,
panel.grid.major.x = element_blank())+
labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)
ggsave('FAM86A tcga by Lauren.svg',dpi=300, width=4,units = "in")
ggsave('FAM86A TCGA Lauren2.png',dpi=500,width = 1500,units = "px")
kruskal.test(log2.FAM86A ~ Lauren2, data = sub_rse)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by Lauren2
## Kruskal-Wallis chi-squared = 11.864, df = 2, p-value = 0.002653pairwise.wilcox.test(sub_rse$log2.FAM86A, sub_rse$Lauren2,
p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: sub_rse$log2.FAM86A and sub_rse$Lauren2
##
## Diffuse Intestinal
## Intestinal 0.0016 -
## Mixed 0.4017 0.4017
##
## P value adjustment method: BH#Mol.sub
colnames(sub_rse)[16] #"Mol..Sub"## [1] "Mol..Sub"sub_rse<-sub_rse %>%
mutate(mol_tcga = case_when(Mol..Sub == 'CIN' ~ 'CIN',
Mol..Sub == 'EBV' ~ 'EBV',
Mol..Sub == 'GS' ~ 'GS',
Mol..Sub == 'MSI' ~ 'MSI'))
ggplot(data=subset(sub_rse, !is.na(mol_tcga)),aes(x=mol_tcga,y=log2.FAM86A,fill=mol_tcga))+
stat_boxplot(geom ='errorbar',width=.2) +
geom_jitter(colour='gray90',alpha=.8,width = .2)+
geom_boxplot(width=.6)+
theme_Publication()+
scale_fill_aziz()+
scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
theme(axis.text = element_text(family = "Arial",color="black"),
axis.title.y = element_text(vjust = 2.5),
axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
legend.position = 'none',
aspect.ratio = 1.5,
panel.grid.major.x = element_blank())+
labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)
ggsave('FAM86A tcga by mol_tcga.svg',dpi=300, width=4,units = "in")
kruskal.test(log2.FAM86A ~ mol_tcga, data = sub_rse)##
## Kruskal-Wallis rank sum test
##
## data: log2.FAM86A by mol_tcga
## Kruskal-Wallis chi-squared = 19.22, df = 3, p-value = 0.0002462pairwise.wilcox.test(sub_rse$log2.FAM86A, sub_rse$mol_tcga,paired=FALSE,
p.adjust.method = "BH")##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: sub_rse$log2.FAM86A and sub_rse$mol_tcga
##
## CIN EBV GS
## EBV 0.04036 - -
## GS 0.02782 0.57278 -
## MSI 0.22058 0.00258 0.00011
##
## P value adjustment method: BHggsave('FAM86A TCGA sub tcga.png',dpi=500,width = 1250,units = "px")